PDB Short entry for 3HG2 HEADER HYDROLASE 13-MAY-09 3HG2 TITLE HUMAN ALPHA-GALACTOSIDASE CATALYTIC MECHANISM 1. EMPTY ACTIVE SITE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA-GALACTOSIDASE A; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: ALPHA-D-GALACTOSIDE GALACTOHYDROLASE, ALPHA-D-GALACTOSIDASE COMPND 5 A, MELIBIASE; COMPND 6 EC: 3.2.1.22; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: GLA; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS GLYCOPROTEIN, CARBOHYDRATE-BINDING PROTEIN, GLYCOSIDASE, LYSOSOMAL KEYWDS 2 ENZYME, (BETA/ALPHA)8 BARREL, DISEASE MUTATION, DISULFIDE BOND, KEYWDS 3 HYDROLASE, LYSOSOME EXPDTA X-RAY DIFFRACTION AUTHOR A.I.GUCE,N.E.CLARK,S.C.GARMAN REVDAT 6 06-SEP-23 3HG2 1 HETSYN REVDAT 5 29-JUL-20 3HG2 1 COMPND REMARK HETNAM LINK REVDAT 5 2 1 SITE ATOM REVDAT 4 01-NOV-17 3HG2 1 REMARK REVDAT 3 13-JUL-11 3HG2 1 VERSN REVDAT 2 23-FEB-10 3HG2 1 JRNL REVDAT 1 24-NOV-09 3HG2 0 JRNL AUTH A.I.GUCE,N.E.CLARK,E.N.SALGADO,D.R.IVANEN,A.A.KULMINSKAYA, JRNL AUTH 2 H.BRUMER,S.C.GARMAN JRNL TITL CATALYTIC MECHANISM OF HUMAN ALPHA-GALACTOSIDASE. JRNL REF J.BIOL.CHEM. V. 285 3625 2010 JRNL REFN ISSN 0021-9258 JRNL PMID 19940122 JRNL DOI 10.1074/JBC.M109.060145 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.31 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 3 NUMBER OF REFLECTIONS : 45598 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 + TEST SET) : 0.178 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.202 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2339 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3071 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.18 REMARK 3 BIN R VALUE (WORKING SET) : 0.2200 REMARK 3 BIN FREE R VALUE SET COUNT : 168 REMARK 3 BIN FREE R VALUE : 0.2710 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6253 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 183 REMARK 3 SOLVENT ATOMS : 329 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 46.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.47 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.01000 REMARK 3 B22 (A**2) : -0.01000 REMARK 3 B33 (A**2) : 0.01000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.270 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.188 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.131 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 10.432 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.955 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.945 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6627 ; 0.008 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9019 ; 1.128 ; 1.967 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 779 ; 5.759 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 319 ;36.692 ;24.295 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1050 ;14.208 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 38 ;12.311 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 951 ; 0.078 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5064 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2997 ; 0.187 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 4423 ; 0.303 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 436 ; 0.110 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 26 ; 0.202 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 6 ; 0.093 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 4019 ; 0.340 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6226 ; 0.564 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3086 ; 0.927 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2793 ; 1.579 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : 2 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 32 A 328 4 REMARK 3 1 B 32 B 328 4 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 1 A (A): 2387 ; 0.330 ; 0.500 REMARK 3 MEDIUM THERMAL 1 A (A**2): 2387 ; 0.330 ; 2.000 REMARK 3 REMARK 3 NCS GROUP NUMBER : 2 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 329 A 421 4 REMARK 3 1 B 329 B 421 4 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 2 A (A): 735 ; 0.430 ; 0.500 REMARK 3 MEDIUM THERMAL 2 A (A**2): 735 ; 0.340 ; 2.000 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3HG2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-MAY-09. REMARK 100 THE DEPOSITION ID IS D_1000053089. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RUH3R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : OSMIC BLUE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 45612 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 200 DATA REDUNDANCY : 14.00 REMARK 200 R MERGE (I) : 0.11500 REMARK 200 R SYM (I) : 0.11500 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 25.4770 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.4 REMARK 200 DATA REDUNDANCY IN SHELL : 14.20 REMARK 200 R MERGE FOR SHELL (I) : 0.81800 REMARK 200 R SYM FOR SHELL (I) : 0.81800 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB ENTRY 1R46 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.85 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG4000, AMMONIUM SULFATE, SODIUM REMARK 280 ACETATE, PH 4.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 144.77733 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 72.38867 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 72.38867 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 144.77733 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5310 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30670 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E 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 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 GLN A 422 REMARK 465 MET A 423 REMARK 465 SER A 424 REMARK 465 LEU A 425 REMARK 465 LYS A 426 REMARK 465 ASP A 427 REMARK 465 LEU A 428 REMARK 465 LEU A 429 REMARK 465 MET B 423 REMARK 465 SER B 424 REMARK 465 LEU B 425 REMARK 465 LYS B 426 REMARK 465 ASP B 427 REMARK 465 LEU B 428 REMARK 465 LEU B 429 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 MET A 51 -137.98 63.04 REMARK 500 CYS A 52 50.06 -114.37 REMARK 500 ASP A 92 -149.55 -101.91 REMARK 500 CYS A 94 33.86 77.59 REMARK 500 ASP A 233 -169.53 -129.85 REMARK 500 ASP A 266 179.20 92.76 REMARK 500 ASN A 272 -130.79 -98.05 REMARK 500 ASP A 313 106.56 -57.49 REMARK 500 MET B 51 -132.61 53.07 REMARK 500 ASP B 92 -151.70 -96.91 REMARK 500 CYS B 94 36.16 80.59 REMARK 500 ASP B 266 178.91 88.79 REMARK 500 ASN B 272 -124.78 -97.96 REMARK 500 GLU B 358 40.20 -107.27 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3HG3 RELATED DB: PDB REMARK 900 HUMAN ALPHA-GALACTOSIDASE MECHANISM 2. SUBSTRATE BOUND REMARK 900 RELATED ID: 3HG4 RELATED DB: PDB REMARK 900 HUMAN ALPHA-GALACTOSIDASE MECHANISM 3. COVALENT INTERMEDIATE REMARK 900 RELATED ID: 3HG5 RELATED DB: PDB REMARK 900 HUMAN ALPHA-GALACTOSIDASE MECHANISM 4. PRODUCT BOUND REMARK 900 RELATED ID: 1R46 RELATED DB: PDB REMARK 900 RELATED ID: 1R47 RELATED DB: PDB DBREF 3HG2 A 32 429 UNP P06280 AGAL_HUMAN 32 429 DBREF 3HG2 B 32 429 UNP P06280 AGAL_HUMAN 32 429 SEQRES 1 A 398 LEU ASP ASN GLY LEU ALA ARG THR PRO THR MET GLY TRP SEQRES 2 A 398 LEU HIS TRP GLU ARG PHE MET CYS ASN LEU ASP CYS GLN SEQRES 3 A 398 GLU GLU PRO ASP SER CYS ILE SER GLU LYS LEU PHE MET SEQRES 4 A 398 GLU MET ALA GLU LEU MET VAL SER GLU GLY TRP LYS ASP SEQRES 5 A 398 ALA GLY TYR GLU TYR LEU CYS ILE ASP ASP CYS TRP MET SEQRES 6 A 398 ALA PRO GLN ARG ASP SER GLU GLY ARG LEU GLN ALA ASP SEQRES 7 A 398 PRO GLN ARG PHE PRO HIS GLY ILE ARG GLN LEU ALA ASN SEQRES 8 A 398 TYR VAL HIS SER LYS GLY LEU LYS LEU GLY ILE TYR ALA SEQRES 9 A 398 ASP VAL GLY ASN LYS THR CYS ALA GLY PHE PRO GLY SER SEQRES 10 A 398 PHE GLY TYR TYR ASP ILE ASP ALA GLN THR PHE ALA ASP SEQRES 11 A 398 TRP GLY VAL ASP LEU LEU LYS PHE ASP GLY CYS TYR CYS SEQRES 12 A 398 ASP SER LEU GLU ASN LEU ALA ASP GLY TYR LYS HIS MET SEQRES 13 A 398 SER LEU ALA LEU ASN ARG THR GLY ARG SER ILE VAL TYR SEQRES 14 A 398 SER CYS GLU TRP PRO LEU TYR MET TRP PRO PHE GLN LYS SEQRES 15 A 398 PRO ASN TYR THR GLU ILE ARG GLN TYR CYS ASN HIS TRP SEQRES 16 A 398 ARG ASN PHE ALA ASP ILE ASP ASP SER TRP LYS SER ILE SEQRES 17 A 398 LYS SER ILE LEU ASP TRP THR SER PHE ASN GLN GLU ARG SEQRES 18 A 398 ILE VAL ASP VAL ALA GLY PRO GLY GLY TRP ASN ASP PRO SEQRES 19 A 398 ASP MET LEU VAL ILE GLY ASN PHE GLY LEU SER TRP ASN SEQRES 20 A 398 GLN GLN VAL THR GLN MET ALA LEU TRP ALA ILE MET ALA SEQRES 21 A 398 ALA PRO LEU PHE MET SER ASN ASP LEU ARG HIS ILE SER SEQRES 22 A 398 PRO GLN ALA LYS ALA LEU LEU GLN ASP LYS ASP VAL ILE SEQRES 23 A 398 ALA ILE ASN GLN ASP PRO LEU GLY LYS GLN GLY TYR GLN SEQRES 24 A 398 LEU ARG GLN GLY ASP ASN PHE GLU VAL TRP GLU ARG PRO SEQRES 25 A 398 LEU SER GLY LEU ALA TRP ALA VAL ALA MET ILE ASN ARG SEQRES 26 A 398 GLN GLU ILE GLY GLY PRO ARG SER TYR THR ILE ALA VAL SEQRES 27 A 398 ALA SER LEU GLY LYS GLY VAL ALA CYS ASN PRO ALA CYS SEQRES 28 A 398 PHE ILE THR GLN LEU LEU PRO VAL LYS ARG LYS LEU GLY SEQRES 29 A 398 PHE TYR GLU TRP THR SER ARG LEU ARG SER HIS ILE ASN SEQRES 30 A 398 PRO THR GLY THR VAL LEU LEU GLN LEU GLU ASN THR MET SEQRES 31 A 398 GLN MET SER LEU LYS ASP LEU LEU SEQRES 1 B 398 LEU ASP ASN GLY LEU ALA ARG THR PRO THR MET GLY TRP SEQRES 2 B 398 LEU HIS TRP GLU ARG PHE MET CYS ASN LEU ASP CYS GLN SEQRES 3 B 398 GLU GLU PRO ASP SER CYS ILE SER GLU LYS LEU PHE MET SEQRES 4 B 398 GLU MET ALA GLU LEU MET VAL SER GLU GLY TRP LYS ASP SEQRES 5 B 398 ALA GLY TYR GLU TYR LEU CYS ILE ASP ASP CYS TRP MET SEQRES 6 B 398 ALA PRO GLN ARG ASP SER GLU GLY ARG LEU GLN ALA ASP SEQRES 7 B 398 PRO GLN ARG PHE PRO HIS GLY ILE ARG GLN LEU ALA ASN SEQRES 8 B 398 TYR VAL HIS SER LYS GLY LEU LYS LEU GLY ILE TYR ALA SEQRES 9 B 398 ASP VAL GLY ASN LYS THR CYS ALA GLY PHE PRO GLY SER SEQRES 10 B 398 PHE GLY TYR TYR ASP ILE ASP ALA GLN THR PHE ALA ASP SEQRES 11 B 398 TRP GLY VAL ASP LEU LEU LYS PHE ASP GLY CYS TYR CYS SEQRES 12 B 398 ASP SER LEU GLU ASN LEU ALA ASP GLY TYR LYS HIS MET SEQRES 13 B 398 SER LEU ALA LEU ASN ARG THR GLY ARG SER ILE VAL TYR SEQRES 14 B 398 SER CYS GLU TRP PRO LEU TYR MET TRP PRO PHE GLN LYS SEQRES 15 B 398 PRO ASN TYR THR GLU ILE ARG GLN TYR CYS ASN HIS TRP SEQRES 16 B 398 ARG ASN PHE ALA ASP ILE ASP ASP SER TRP LYS SER ILE SEQRES 17 B 398 LYS SER ILE LEU ASP TRP THR SER PHE ASN GLN GLU ARG SEQRES 18 B 398 ILE VAL ASP VAL ALA GLY PRO GLY GLY TRP ASN ASP PRO SEQRES 19 B 398 ASP MET LEU VAL ILE GLY ASN PHE GLY LEU SER TRP ASN SEQRES 20 B 398 GLN GLN VAL THR GLN MET ALA LEU TRP ALA ILE MET ALA SEQRES 21 B 398 ALA PRO LEU PHE MET SER ASN ASP LEU ARG HIS ILE SER SEQRES 22 B 398 PRO GLN ALA LYS ALA LEU LEU GLN ASP LYS ASP VAL ILE SEQRES 23 B 398 ALA ILE ASN GLN ASP PRO LEU GLY LYS GLN GLY TYR GLN SEQRES 24 B 398 LEU ARG GLN GLY ASP ASN PHE GLU VAL TRP GLU ARG PRO SEQRES 25 B 398 LEU SER GLY LEU ALA TRP ALA VAL ALA MET ILE ASN ARG SEQRES 26 B 398 GLN GLU ILE GLY GLY PRO ARG SER TYR THR ILE ALA VAL SEQRES 27 B 398 ALA SER LEU GLY LYS GLY VAL ALA CYS ASN PRO ALA CYS SEQRES 28 B 398 PHE ILE THR GLN LEU LEU PRO VAL LYS ARG LYS LEU GLY SEQRES 29 B 398 PHE TYR GLU TRP THR SER ARG LEU ARG SER HIS ILE ASN SEQRES 30 B 398 PRO THR GLY THR VAL LEU LEU GLN LEU GLU ASN THR MET SEQRES 31 B 398 GLN MET SER LEU LYS ASP LEU LEU MODRES 3HG2 ASN A 139 ASN GLYCOSYLATION SITE MODRES 3HG2 ASN A 192 ASN GLYCOSYLATION SITE MODRES 3HG2 ASN A 215 ASN GLYCOSYLATION SITE MODRES 3HG2 ASN B 139 ASN GLYCOSYLATION SITE MODRES 3HG2 ASN B 192 ASN GLYCOSYLATION SITE MODRES 3HG2 ASN B 215 ASN GLYCOSYLATION SITE HET NAG C 1 14 HET FUC C 2 10 HET NAG D 1 14 HET NAG D 2 14 HET BMA D 3 11 HET NAG E 1 14 HET NAG E 2 14 HET BMA E 3 11 HET NAG A 715 14 HET SO4 A 822 5 HET SO4 A 823 5 HET ACY A 841 4 HET NAG B 639 14 HET NAG B 715 14 HET GAL B 803 12 HET SO4 B 821 5 HET ACY B 842 4 HET ACY B 843 4 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM FUC ALPHA-L-FUCOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE HETNAM SO4 SULFATE ION HETNAM ACY ACETIC ACID HETNAM GAL BETA-D-GALACTOPYRANOSE HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE HETSYN FUC ALPHA-L-FUCOSE; 6-DEOXY-ALPHA-L-GALACTOPYRANOSE; L- HETSYN 2 FUC FUCOSE; FUCOSE HETSYN BMA BETA-D-MANNOSE; D-MANNOSE; MANNOSE HETSYN GAL BETA-D-GALACTOSE; D-GALACTOSE; GALACTOSE FORMUL 3 NAG 8(C8 H15 N O6) FORMUL 3 FUC C6 H12 O5 FORMUL 4 BMA 2(C6 H12 O6) FORMUL 7 SO4 3(O4 S 2-) FORMUL 9 ACY 3(C2 H4 O2) FORMUL 12 GAL C6 H12 O6 FORMUL 16 HOH *329(H2 O) HELIX 1 1 HIS A 46 MET A 51 1 6 HELIX 2 2 SER A 65 GLU A 79 1 15 HELIX 3 3 GLY A 80 GLY A 85 1 6 HELIX 4 4 GLY A 116 LYS A 127 1 12 HELIX 5 5 TYR A 151 GLY A 163 1 13 HELIX 6 6 SER A 176 GLY A 195 1 20 HELIX 7 7 GLU A 203 TRP A 209 1 7 HELIX 8 8 ASN A 215 CYS A 223 1 9 HELIX 9 9 SER A 235 ASN A 249 1 15 HELIX 10 10 ASN A 249 VAL A 254 1 6 HELIX 11 11 SER A 276 MET A 290 1 15 HELIX 12 12 SER A 304 GLN A 312 1 9 HELIX 13 13 ASP A 313 GLN A 321 1 9 HELIX 14 14 ALA A 370 VAL A 376 5 7 HELIX 15 15 HIS B 46 MET B 51 1 6 HELIX 16 16 SER B 65 GLU B 79 1 15 HELIX 17 17 GLY B 80 GLY B 85 1 6 HELIX 18 18 HIS B 115 LYS B 127 1 13 HELIX 19 19 TYR B 151 GLY B 163 1 13 HELIX 20 20 SER B 176 ARG B 193 1 18 HELIX 21 21 GLU B 203 TRP B 209 1 7 HELIX 22 22 ASN B 215 CYS B 223 1 9 HELIX 23 23 SER B 235 ASN B 249 1 15 HELIX 24 24 ASN B 249 VAL B 254 1 6 HELIX 25 25 SER B 276 MET B 290 1 15 HELIX 26 26 SER B 304 GLN B 312 1 9 HELIX 27 27 ASP B 313 GLN B 321 1 9 HELIX 28 28 SER B 345 LEU B 347 5 3 HELIX 29 29 ALA B 370 VAL B 376 5 7 SHEET 1 A 8 TRP A 262 ASP A 264 0 SHEET 2 A 8 HIS A 225 ARG A 227 1 N TRP A 226 O ASP A 264 SHEET 3 A 8 VAL A 199 CYS A 202 1 N CYS A 202 O HIS A 225 SHEET 4 A 8 LEU A 166 ASP A 170 1 N LEU A 167 O SER A 201 SHEET 5 A 8 LYS A 130 ASP A 136 1 N ALA A 135 O ASP A 170 SHEET 6 A 8 TYR A 88 CYS A 90 1 N LEU A 89 O LYS A 130 SHEET 7 A 8 MET A 42 LEU A 45 1 N TRP A 44 O CYS A 90 SHEET 8 A 8 LEU A 294 MET A 296 1 O MET A 296 N LEU A 45 SHEET 1 B 6 TYR A 329 GLY A 334 0 SHEET 2 B 6 PHE A 337 PRO A 343 -1 O VAL A 339 N LEU A 331 SHEET 3 B 6 ALA A 348 ASN A 355 -1 O ALA A 352 N TRP A 340 SHEET 4 B 6 THR A 412 ASN A 419 -1 O LEU A 415 N VAL A 351 SHEET 5 B 6 ALA A 381 LEU A 388 -1 N LEU A 387 O LEU A 414 SHEET 6 B 6 ARG A 392 GLU A 398 -1 O ARG A 392 N GLN A 386 SHEET 1 C 2 ARG A 363 ALA A 368 0 SHEET 2 C 2 ARG A 402 ILE A 407 -1 O SER A 405 N TYR A 365 SHEET 1 D 8 TRP B 262 ASP B 264 0 SHEET 2 D 8 HIS B 225 ARG B 227 1 N TRP B 226 O ASP B 264 SHEET 3 D 8 VAL B 199 CYS B 202 1 N CYS B 202 O HIS B 225 SHEET 4 D 8 LEU B 166 ASP B 170 1 N LEU B 167 O VAL B 199 SHEET 5 D 8 LYS B 130 ASP B 136 1 N ALA B 135 O ASP B 170 SHEET 6 D 8 TYR B 88 CYS B 90 1 N LEU B 89 O LYS B 130 SHEET 7 D 8 MET B 42 LEU B 45 1 N TRP B 44 O CYS B 90 SHEET 8 D 8 LEU B 294 MET B 296 1 O MET B 296 N LEU B 45 SHEET 1 E 6 TYR B 329 GLY B 334 0 SHEET 2 E 6 PHE B 337 PRO B 343 -1 O VAL B 339 N ARG B 332 SHEET 3 E 6 TRP B 349 ASN B 355 -1 O ALA B 352 N TRP B 340 SHEET 4 E 6 THR B 412 THR B 420 -1 O LEU B 417 N TRP B 349 SHEET 5 E 6 ALA B 381 LEU B 388 -1 N LEU B 387 O LEU B 414 SHEET 6 E 6 ARG B 392 GLU B 398 -1 O ARG B 392 N GLN B 386 SHEET 1 F 2 ARG B 363 ALA B 368 0 SHEET 2 F 2 ARG B 402 ILE B 407 -1 O LEU B 403 N ILE B 367 SSBOND 1 CYS A 52 CYS A 94 1555 1555 2.02 SSBOND 2 CYS A 56 CYS A 63 1555 1555 2.03 SSBOND 3 CYS A 142 CYS A 172 1555 1555 2.03 SSBOND 4 CYS A 202 CYS A 223 1555 1555 2.03 SSBOND 5 CYS A 378 CYS A 382 1555 1555 2.03 SSBOND 6 CYS B 52 CYS B 94 1555 1555 2.03 SSBOND 7 CYS B 56 CYS B 63 1555 1555 2.03 SSBOND 8 CYS B 142 CYS B 172 1555 1555 2.03 SSBOND 9 CYS B 202 CYS B 223 1555 1555 2.04 SSBOND 10 CYS B 378 CYS B 382 1555 1555 2.03 LINK ND2 ASN A 139 C1 NAG C 1 1555 1555 1.45 LINK ND2 ASN A 192 C1 NAG D 1 1555 1555 1.44 LINK ND2 ASN A 215 C1 NAG A 715 1555 1555 1.45 LINK ND2 ASN B 139 C1 NAG B 639 1555 1555 1.45 LINK ND2 ASN B 192 C1 NAG E 1 1555 1555 1.44 LINK ND2 ASN B 215 C1 NAG B 715 1555 1555 1.45 LINK O6 NAG C 1 C1 FUC C 2 1555 1555 1.44 LINK O4 NAG D 1 C1 NAG D 2 1555 1555 1.44 LINK O4 NAG D 2 C1 BMA D 3 1555 1555 1.44 LINK O4 NAG E 1 C1 NAG E 2 1555 1555 1.44 LINK O4 NAG E 2 C1 BMA E 3 1555 1555 1.46 CISPEP 1 ASN A 379 PRO A 380 0 -0.26 CISPEP 2 LEU A 388 PRO A 389 0 1.40 CISPEP 3 ASN B 379 PRO B 380 0 2.34 CISPEP 4 LEU B 388 PRO B 389 0 2.44 CRYST1 90.813 90.813 217.166 90.00 90.00 120.00 P 32 2 1 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 0.011012 0.006358 0.000000 0.00000 SCALE2 0.000000 0.012715 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004605 0.00000