PDB Short entry for 1TJJ HEADER SIGNALING PROTEIN 04-JUN-04 1TJJ TITLE HUMAN GM2 ACTIVATOR PROTEIN PAF COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: GANGLIOSIDE GM2 ACTIVATOR; COMPND 3 CHAIN: A, B, C; COMPND 4 SYNONYM: GM2-AP, CEREBROSIDE SULFATE ACTIVATOR PROTEIN, SHINGOLIPID COMPND 5 ACTIVATOR PROTEIN 3, SAP-3; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 ORGAN: LIVER,PLACENTA,KIDNEY,BRAIN; SOURCE 6 GENE: GM2A; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET16B(NOVAGEN) KEYWDS PLATELET ACTIVATING FACTOR, LIPID BINDING POCKET, BETA-CUP TOPOLOGY, KEYWDS 2 PROTEIN DYNAMICS, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.S.WRIGHT,L.-Z.MI,F.RASTINEJAD REVDAT 3 16-OCT-13 1TJJ 1 HETATM VERSN REVDAT 2 24-FEB-09 1TJJ 1 VERSN REVDAT 1 07-DEC-04 1TJJ 0 JRNL AUTH C.S.WRIGHT,L.-Z.MI,F.RASTINEJAD JRNL TITL EVIDENCE FOR LIPID PACKAGING IN THE CRYSTAL STRUCTURE OF THE JRNL TITL 2 GM2-ACTIVATOR COMPLEX WITH PLATELET ACTIVATING FACTOR JRNL REF J.MOL.BIOL. V. 342 585 2004 JRNL REFN ISSN 0022-2836 JRNL PMID 15327957 JRNL DOI 10.1016/J.JMB.2004.07.063 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.79 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1894751.390 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 44841 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.300 REMARK 3 FREE R VALUE TEST SET COUNT : 3727 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.004 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.13 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.30 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 6337 REMARK 3 BIN R VALUE (WORKING SET) : 0.1840 REMARK 3 BIN FREE R VALUE : 0.2400 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 8.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 570 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.010 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3716 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 294 REMARK 3 SOLVENT ATOMS : 568 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 10.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.29000 REMARK 3 B22 (A**2) : -0.42000 REMARK 3 B33 (A**2) : -0.87000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.20 REMARK 3 ESD FROM SIGMAA (A) : 0.01 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.26 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.10 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.50 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.00 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 2.640 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.610 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 10.020; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 7.100 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.35 REMARK 3 BSOL : 63.58 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : ION.PARAM REMARK 3 PARAMETER FILE 3 : SOLVENT_REP.PARAM REMARK 3 PARAMETER FILE 4 : PAF_LPE_EPE_LAU.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : ION.TOP REMARK 3 TOPOLOGY FILE 3 : SOLVENT.TOP REMARK 3 TOPOLOGY FILE 4 : PAF_LPE_EPE_LAU.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1TJJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-JUN-04. REMARK 100 THE RCSB ID CODE IS RCSB022689. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-AUG-03 REMARK 200 TEMPERATURE (KELVIN) : 123 REMARK 200 PH : 7.9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 17-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : CCP4 (TRUNCATE) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44841 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 4.900 REMARK 200 R MERGE (I) : 0.04500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 29.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.90 REMARK 200 R MERGE FOR SHELL (I) : 0.10400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 16.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.94 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG4000, ISO-PROPANOL, HEPES BUFFER, REMARK 280 PH 7.9, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 278K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 31.73500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 60.23500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.25500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 60.23500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 31.73500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 43.25500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4, 5, 6 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 4 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 13170 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25520 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -92.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 5 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7000 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19670 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -62.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 63.47000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 -43.25500 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 60.23500 REMARK 350 REMARK 350 BIOMOLECULE: 6 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6980 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19700 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -58.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 63.47000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 43.25500 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 60.23500 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 HIS C 1 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 HIS A 1 CB CG ND1 CD2 CE1 NE2 REMARK 470 HIS B 1 CB CG ND1 CD2 CE1 NE2 REMARK 470 MET C 2 CG SD CE REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASP A 11 68.41 -153.69 REMARK 500 TYR A 73 -1.58 73.78 REMARK 500 TYR B 73 -6.40 70.32 REMARK 500 CYS B 107 20.49 -143.43 REMARK 500 SER C 3 -166.06 -76.52 REMARK 500 GLU C 12 -72.19 -36.60 REMARK 500 CYS C 107 27.28 -146.70 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A3408 DISTANCE = 5.02 ANGSTROMS REMARK 525 HOH A3485 DISTANCE = 5.79 ANGSTROMS REMARK 525 HOH A3493 DISTANCE = 7.42 ANGSTROMS REMARK 525 HOH A3498 DISTANCE = 5.69 ANGSTROMS REMARK 525 HOH A3502 DISTANCE = 6.75 ANGSTROMS REMARK 525 HOH B3346 DISTANCE = 6.73 ANGSTROMS REMARK 525 HOH B3489 DISTANCE = 5.49 ANGSTROMS REMARK 525 HOH B3490 DISTANCE = 5.30 ANGSTROMS REMARK 525 HOH B3511 DISTANCE = 5.30 ANGSTROMS REMARK 525 HOH B3512 DISTANCE = 5.36 ANGSTROMS REMARK 525 HOH C3485 DISTANCE = 5.53 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 3320 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 3321 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B 3322 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B 3323 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT C 3324 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 802 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL C 803 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EPE A 900 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EPE C 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PFS A 2482 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PFS B 2484 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PFS C 2486 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE LPE A 2483 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE LPE B 2485 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE LPE C 2488 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DAO B 1364 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IPA A 1503 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IPA C 1511 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IPA C 1514 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IPA B 1515 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1G13 RELATED DB: PDB REMARK 900 APO STRUCTURE REMARK 900 RELATED ID: 1PUB RELATED DB: PDB REMARK 900 APO STRUCTURE, DIFF. CRYSTAL FORM REMARK 900 RELATED ID: 1PU5 RELATED DB: PDB REMARK 900 GM2-GANGLIOSIDE-PROTEIN COMPLEX DBREF 1TJJ A 3 164 UNP P17900 SAP3_HUMAN 31 192 DBREF 1TJJ B 3 164 UNP P17900 SAP3_HUMAN 31 192 DBREF 1TJJ C 3 164 UNP P17900 SAP3_HUMAN 31 192 SEQADV 1TJJ HIS A 1 UNP P17900 EXPRESSION TAG SEQADV 1TJJ MET A 2 UNP P17900 EXPRESSION TAG SEQADV 1TJJ HIS B 1 UNP P17900 EXPRESSION TAG SEQADV 1TJJ MET B 2 UNP P17900 EXPRESSION TAG SEQADV 1TJJ HIS C 1 UNP P17900 EXPRESSION TAG SEQADV 1TJJ MET C 2 UNP P17900 EXPRESSION TAG SEQRES 1 A 164 HIS MET SER SER PHE SER TRP ASP ASN CYS ASP GLU GLY SEQRES 2 A 164 LYS ASP PRO ALA VAL ILE ARG SER LEU THR LEU GLU PRO SEQRES 3 A 164 ASP PRO ILE VAL VAL PRO GLY ASN VAL THR LEU SER VAL SEQRES 4 A 164 VAL GLY SER THR SER VAL PRO LEU SER SER PRO LEU LYS SEQRES 5 A 164 VAL ASP LEU VAL LEU GLU LYS GLU VAL ALA GLY LEU TRP SEQRES 6 A 164 ILE LYS ILE PRO CYS THR ASP TYR ILE GLY SER CYS THR SEQRES 7 A 164 PHE GLU HIS PHE CYS ASP VAL LEU ASP MET LEU ILE PRO SEQRES 8 A 164 THR GLY GLU PRO CYS PRO GLU PRO LEU ARG THR TYR GLY SEQRES 9 A 164 LEU PRO CYS HIS CYS PRO PHE LYS GLU GLY THR TYR SER SEQRES 10 A 164 LEU PRO LYS SER GLU PHE VAL VAL PRO ASP LEU GLU LEU SEQRES 11 A 164 PRO SER TRP LEU THR THR GLY ASN TYR ARG ILE GLU SER SEQRES 12 A 164 VAL LEU SER SER SER GLY LYS ARG LEU GLY CYS ILE LYS SEQRES 13 A 164 ILE ALA ALA SER LEU LYS GLY ILE SEQRES 1 B 164 HIS MET SER SER PHE SER TRP ASP ASN CYS ASP GLU GLY SEQRES 2 B 164 LYS ASP PRO ALA VAL ILE ARG SER LEU THR LEU GLU PRO SEQRES 3 B 164 ASP PRO ILE VAL VAL PRO GLY ASN VAL THR LEU SER VAL SEQRES 4 B 164 VAL GLY SER THR SER VAL PRO LEU SER SER PRO LEU LYS SEQRES 5 B 164 VAL ASP LEU VAL LEU GLU LYS GLU VAL ALA GLY LEU TRP SEQRES 6 B 164 ILE LYS ILE PRO CYS THR ASP TYR ILE GLY SER CYS THR SEQRES 7 B 164 PHE GLU HIS PHE CYS ASP VAL LEU ASP MET LEU ILE PRO SEQRES 8 B 164 THR GLY GLU PRO CYS PRO GLU PRO LEU ARG THR TYR GLY SEQRES 9 B 164 LEU PRO CYS HIS CYS PRO PHE LYS GLU GLY THR TYR SER SEQRES 10 B 164 LEU PRO LYS SER GLU PHE VAL VAL PRO ASP LEU GLU LEU SEQRES 11 B 164 PRO SER TRP LEU THR THR GLY ASN TYR ARG ILE GLU SER SEQRES 12 B 164 VAL LEU SER SER SER GLY LYS ARG LEU GLY CYS ILE LYS SEQRES 13 B 164 ILE ALA ALA SER LEU LYS GLY ILE SEQRES 1 C 164 HIS MET SER SER PHE SER TRP ASP ASN CYS ASP GLU GLY SEQRES 2 C 164 LYS ASP PRO ALA VAL ILE ARG SER LEU THR LEU GLU PRO SEQRES 3 C 164 ASP PRO ILE VAL VAL PRO GLY ASN VAL THR LEU SER VAL SEQRES 4 C 164 VAL GLY SER THR SER VAL PRO LEU SER SER PRO LEU LYS SEQRES 5 C 164 VAL ASP LEU VAL LEU GLU LYS GLU VAL ALA GLY LEU TRP SEQRES 6 C 164 ILE LYS ILE PRO CYS THR ASP TYR ILE GLY SER CYS THR SEQRES 7 C 164 PHE GLU HIS PHE CYS ASP VAL LEU ASP MET LEU ILE PRO SEQRES 8 C 164 THR GLY GLU PRO CYS PRO GLU PRO LEU ARG THR TYR GLY SEQRES 9 C 164 LEU PRO CYS HIS CYS PRO PHE LYS GLU GLY THR TYR SER SEQRES 10 C 164 LEU PRO LYS SER GLU PHE VAL VAL PRO ASP LEU GLU LEU SEQRES 11 C 164 PRO SER TRP LEU THR THR GLY ASN TYR ARG ILE GLU SER SEQRES 12 C 164 VAL LEU SER SER SER GLY LYS ARG LEU GLY CYS ILE LYS SEQRES 13 C 164 ILE ALA ALA SER LEU LYS GLY ILE HET ACT A3320 4 HET ACT A3321 4 HET ACT B3322 4 HET ACT B3323 4 HET ACT C3324 4 HET CL A 801 1 HET CL B 802 1 HET CL C 803 1 HET EPE A 900 15 HET EPE C 901 15 HET PFS A2482 35 HET PFS B2484 35 HET PFS C2486 35 HET LPE A2483 34 HET LPE B2485 34 HET LPE C2488 34 HET DAO B1364 14 HET IPA A1503 4 HET IPA C1511 4 HET IPA C1513 4 HET IPA C1514 4 HET IPA B1515 4 HETNAM ACT ACETATE ION HETNAM CL CHLORIDE ION HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETNAM PFS (2R)-2-(ACETYLOXY)-3-(HEXADECYLOXY)PROPYL 2- HETNAM 2 PFS (TRIMETHYLAMMONIO)ETHYL PHOSPHATE HETNAM LPE 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE HETNAM DAO LAURIC ACID HETNAM IPA ISOPROPYL ALCOHOL HETSYN EPE HEPES HETSYN PFS PLATELET ACTIVATING FACTOR HETSYN LPE LPC-ETHER HETSYN IPA 2-PROPANOL FORMUL 4 ACT 5(C2 H3 O2 1-) FORMUL 9 CL 3(CL 1-) FORMUL 12 EPE 2(C8 H18 N2 O4 S) FORMUL 14 PFS 3(C26 H54 N O7 P) FORMUL 17 LPE 3(C26 H57 N O6 P 1+) FORMUL 20 DAO C12 H24 O2 FORMUL 21 IPA 5(C3 H8 O) FORMUL 26 HOH *568(H2 O) HELIX 1 1 HIS A 81 ILE A 90 1 10 HELIX 2 2 PRO A 131 THR A 136 1 6 HELIX 3 3 HIS B 81 ILE B 90 1 10 HELIX 4 4 PRO B 131 THR B 136 1 6 HELIX 5 5 HIS C 81 ILE C 90 1 10 HELIX 6 6 PRO C 131 THR C 136 1 6 SHEET 1 A 5 SER A 6 ASN A 9 0 SHEET 2 A 5 LYS A 150 GLY A 163 -1 O LYS A 156 N ASP A 8 SHEET 3 A 5 GLY A 137 SER A 147 -1 N LEU A 145 O GLY A 153 SHEET 4 A 5 LYS A 52 VAL A 61 -1 N LYS A 52 O SER A 146 SHEET 5 A 5 LEU A 64 ILE A 68 -1 O LEU A 64 N VAL A 61 SHEET 1 B 5 ILE A 29 VAL A 31 0 SHEET 2 B 5 LYS A 150 GLY A 163 1 O SER A 160 N ILE A 29 SHEET 3 B 5 GLY A 137 SER A 147 -1 N LEU A 145 O GLY A 153 SHEET 4 B 5 LYS A 52 VAL A 61 -1 N LYS A 52 O SER A 146 SHEET 5 B 5 THR A 78 PHE A 79 -1 O PHE A 79 N VAL A 53 SHEET 1 C 3 ALA A 17 GLU A 25 0 SHEET 2 C 3 ASN A 34 THR A 43 -1 O THR A 36 N GLU A 25 SHEET 3 C 3 GLY A 114 VAL A 124 -1 O TYR A 116 N GLY A 41 SHEET 1 D 5 SER B 6 ASN B 9 0 SHEET 2 D 5 LYS B 150 GLY B 163 -1 O ALA B 158 N SER B 6 SHEET 3 D 5 GLY B 137 SER B 147 -1 N LEU B 145 O LEU B 152 SHEET 4 D 5 LYS B 52 VAL B 61 -1 N LYS B 52 O SER B 146 SHEET 5 D 5 LEU B 64 ILE B 68 -1 O LEU B 64 N VAL B 61 SHEET 1 E 5 ILE B 29 VAL B 31 0 SHEET 2 E 5 LYS B 150 GLY B 163 1 O SER B 160 N ILE B 29 SHEET 3 E 5 GLY B 137 SER B 147 -1 N LEU B 145 O LEU B 152 SHEET 4 E 5 LYS B 52 VAL B 61 -1 N LYS B 52 O SER B 146 SHEET 5 E 5 THR B 78 PHE B 79 -1 O PHE B 79 N VAL B 53 SHEET 1 F 3 ALA B 17 GLU B 25 0 SHEET 2 F 3 GLY B 33 THR B 43 -1 O VAL B 40 N ARG B 20 SHEET 3 F 3 GLY B 114 VAL B 125 -1 O TYR B 116 N GLY B 41 SHEET 1 G 5 SER C 6 ASN C 9 0 SHEET 2 G 5 LYS C 150 LYS C 162 -1 O LYS C 156 N ASP C 8 SHEET 3 G 5 GLY C 137 SER C 147 -1 N TYR C 139 O ALA C 159 SHEET 4 G 5 LYS C 52 VAL C 61 -1 N LYS C 52 O SER C 146 SHEET 5 G 5 LEU C 64 LYS C 67 -1 O LEU C 64 N VAL C 61 SHEET 1 H 5 ILE C 29 VAL C 30 0 SHEET 2 H 5 LYS C 150 LYS C 162 1 O SER C 160 N ILE C 29 SHEET 3 H 5 GLY C 137 SER C 147 -1 N TYR C 139 O ALA C 159 SHEET 4 H 5 LYS C 52 VAL C 61 -1 N LYS C 52 O SER C 146 SHEET 5 H 5 THR C 78 PHE C 79 -1 O PHE C 79 N VAL C 53 SHEET 1 I 3 ALA C 17 GLU C 25 0 SHEET 2 I 3 ASN C 34 THR C 43 -1 O VAL C 40 N ARG C 20 SHEET 3 I 3 GLY C 114 VAL C 124 -1 O TYR C 116 N GLY C 41 SSBOND 1 CYS A 10 CYS A 154 1555 1555 2.06 SSBOND 2 CYS A 70 CYS A 77 1555 1555 2.04 SSBOND 3 CYS A 83 CYS A 109 1555 1555 2.04 SSBOND 4 CYS A 96 CYS A 107 1555 1555 2.06 SSBOND 5 CYS B 10 CYS B 154 1555 1555 2.06 SSBOND 6 CYS B 70 CYS B 77 1555 1555 2.05 SSBOND 7 CYS B 83 CYS B 109 1555 1555 2.04 SSBOND 8 CYS B 96 CYS B 107 1555 1555 2.05 SSBOND 9 CYS C 10 CYS C 154 1555 1555 2.05 SSBOND 10 CYS C 70 CYS C 77 1555 1555 2.06 SSBOND 11 CYS C 83 CYS C 109 1555 1555 2.06 SSBOND 12 CYS C 96 CYS C 107 1555 1555 2.05 CISPEP 1 GLU A 25 PRO A 26 0 -0.45 CISPEP 2 ASP A 27 PRO A 28 0 0.25 CISPEP 3 VAL A 31 PRO A 32 0 -0.22 CISPEP 4 SER A 49 PRO A 50 0 -0.11 CISPEP 5 GLU A 98 PRO A 99 0 0.77 CISPEP 6 CYS A 109 PRO A 110 0 -0.08 CISPEP 7 GLU B 25 PRO B 26 0 -0.26 CISPEP 8 ASP B 27 PRO B 28 0 0.22 CISPEP 9 VAL B 31 PRO B 32 0 -0.34 CISPEP 10 SER B 49 PRO B 50 0 -0.15 CISPEP 11 GLU B 98 PRO B 99 0 0.14 CISPEP 12 CYS B 109 PRO B 110 0 -0.43 CISPEP 13 GLU C 25 PRO C 26 0 -0.20 CISPEP 14 ASP C 27 PRO C 28 0 0.11 CISPEP 15 VAL C 31 PRO C 32 0 -0.27 CISPEP 16 SER C 49 PRO C 50 0 -0.09 CISPEP 17 GLU C 98 PRO C 99 0 0.29 CISPEP 18 CYS C 109 PRO C 110 0 -0.38 SITE 1 AC1 1 LPE A2483 SITE 1 AC2 2 PFS A2482 LPE A2483 SITE 1 AC3 2 PHE B 111 PFS B2484 SITE 1 AC4 2 LPE B2485 HOH B3517 SITE 1 AC5 1 LPE C2488 SITE 1 AC6 6 SER A 49 PRO A 50 LEU A 51 HIS A 81 SITE 2 AC6 6 CYS A 83 HOH C3389 SITE 1 AC7 6 HOH A3456 SER B 49 PRO B 50 LEU B 51 SITE 2 AC7 6 HIS B 81 CYS B 83 SITE 1 AC8 3 LEU C 51 HIS C 81 CYS C 83 SITE 1 AC9 7 SER A 6 TRP A 7 ASP A 8 GLU A 12 SITE 2 AC9 7 HOH A3429 HOH A3450 HOH A3463 SITE 1 BC1 6 SER C 6 TRP C 7 ASP C 8 ASN C 9 SITE 2 BC1 6 GLU C 12 HOH C3500 SITE 1 BC2 19 ILE A 19 LEU A 24 VAL A 39 LEU A 57 SITE 2 BC2 19 ILE A 68 TYR A 116 SER A 117 LEU A 118 SITE 3 BC2 19 TYR A 139 ARG A 140 ILE A 141 ILE A 157 SITE 4 BC2 19 ALA A 158 ALA A 159 LEU A 161 IPA A1503 SITE 5 BC2 19 LPE A2483 ACT A3321 HOH A3474 SITE 1 BC3 17 LEU B 24 LEU B 37 VAL B 39 GLY B 41 SITE 2 BC3 17 LEU B 57 TYR B 116 LEU B 130 TYR B 139 SITE 3 BC3 17 ARG B 140 ILE B 141 ILE B 157 ALA B 158 SITE 4 BC3 17 ALA B 159 DAO B1364 LPE B2485 ACT B3322 SITE 5 BC3 17 HOH B3518 SITE 1 BC4 12 ILE C 19 VAL C 39 LEU C 57 ILE C 68 SITE 2 BC4 12 LEU C 130 TYR C 139 ARG C 140 ILE C 141 SITE 3 BC4 12 ILE C 157 LEU C 161 LPE C2488 HOH C3464 SITE 1 BC5 15 ALA A 17 VAL A 18 VAL A 53 PHE A 82 SITE 2 BC5 15 LEU A 89 PRO A 106 TYR A 116 SER A 143 SITE 3 BC5 15 CYS A 154 ILE A 155 PFS A2482 ACT A3320 SITE 4 BC5 15 ACT A3321 HOH A3324 HOH A3504 SITE 1 BC6 13 ILE B 19 VAL B 53 PHE B 82 PRO B 106 SITE 2 BC6 13 PHE B 111 TYR B 116 SER B 143 VAL B 144 SITE 3 BC6 13 LEU B 145 ILE B 155 PFS B2484 ACT B3323 SITE 4 BC6 13 HOH B3517 SITE 1 BC7 11 VAL C 18 ILE C 19 VAL C 53 PRO C 106 SITE 2 BC7 11 TYR C 116 SER C 143 GLY C 153 CYS C 154 SITE 3 BC7 11 ILE C 155 PFS C2486 ACT C3324 SITE 1 BC8 4 PRO B 97 PHE B 123 VAL B 125 PFS B2484 SITE 1 BC9 2 VAL A 35 PFS A2482 SITE 1 CC1 2 LEU B 64 TYR C 73 SITE 1 CC2 1 PRO C 126 SITE 1 CC3 2 PRO B 110 HOH B3380 CRYST1 63.470 86.510 120.470 90.00 90.00 90.00 P 21 21 21 12 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.015755 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011559 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008301 0.00000