PDB Short entry for 6E8Z HEADER OXIDOREDUCTASE 31-JUL-18 6E8Z TITLE BINARY COMPLEX OF HUMAN GLYCEROL 3-PHOSPHATE DEHYDROGENASE WITH NAD COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLYCEROL-3-PHOSPHATE DEHYDROGENASE [NAD(+)], CYTOPLASMIC; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: GPDH-C; COMPND 5 EC: 1.1.1.8; 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 GENE: GPD1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR L.S.MYDY,A.M.GULICK REVDAT 4 11-OCT-23 6E8Z 1 LINK REVDAT 3 18-DEC-19 6E8Z 1 REMARK REVDAT 2 13-MAR-19 6E8Z 1 JRNL REVDAT 1 30-JAN-19 6E8Z 0 JRNL AUTH L.S.MYDY,J.R.CRISTOBAL,R.D.KATIGBAK,P.BAUER,A.C.REYES, JRNL AUTH 2 S.C.L.KAMERLIN,J.P.RICHARD,A.M.GULICK JRNL TITL HUMAN GLYCEROL 3-PHOSPHATE DEHYDROGENASE: X-RAY CRYSTAL JRNL TITL 2 STRUCTURES THAT GUIDE THE INTERPRETATION OF MUTAGENESIS JRNL TITL 3 STUDIES. JRNL REF BIOCHEMISTRY V. 58 1061 2019 JRNL REFN ISSN 1520-4995 JRNL PMID 30640445 JRNL DOI 10.1021/ACS.BIOCHEM.8B01103 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.12_2829) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.96 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.070 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.1 REMARK 3 NUMBER OF REFLECTIONS : 37372 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.172 REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.650 REMARK 3 FREE R VALUE TEST SET COUNT : 3284 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 36.1136 - 5.9636 0.96 2975 198 0.1649 0.1846 REMARK 3 2 5.9636 - 4.7369 0.93 2978 104 0.1437 0.1990 REMARK 3 3 4.7369 - 4.1391 0.97 3033 174 0.1236 0.1673 REMARK 3 4 4.1391 - 3.7611 0.92 2903 117 0.1454 0.1447 REMARK 3 5 3.7611 - 3.4917 0.95 3017 135 0.1526 0.2374 REMARK 3 6 3.4917 - 3.2860 0.95 2982 115 0.1713 0.2179 REMARK 3 7 3.2860 - 3.1215 0.96 3049 159 0.1819 0.2482 REMARK 3 8 3.1215 - 2.9857 0.94 2929 167 0.1725 0.2218 REMARK 3 9 2.9857 - 2.8708 0.88 2785 145 0.1783 0.2681 REMARK 3 10 2.8708 - 2.7718 0.92 2862 150 0.1802 0.2576 REMARK 3 11 2.7718 - 2.6852 0.94 2974 126 0.1861 0.2353 REMARK 3 12 2.6852 - 2.6084 0.94 2969 136 0.1783 0.2703 REMARK 3 13 2.6084 - 2.5398 0.94 2937 168 0.1854 0.2371 REMARK 3 14 2.5398 - 2.4778 0.94 2994 136 0.1723 0.2323 REMARK 3 15 2.4778 - 2.4215 0.91 2823 162 0.1824 0.2729 REMARK 3 16 2.4215 - 2.3700 0.88 2740 149 0.1922 0.2604 REMARK 3 17 2.3700 - 2.3226 0.90 2846 111 0.1999 0.2875 REMARK 3 18 2.3226 - 2.2788 0.93 2956 153 0.2074 0.3091 REMARK 3 19 2.2788 - 2.2381 0.92 2891 148 0.2127 0.2665 REMARK 3 20 2.2381 - 2.2002 0.93 2943 112 0.2205 0.3265 REMARK 3 21 2.2002 - 2.1647 0.93 2974 137 0.2312 0.3559 REMARK 3 22 2.1647 - 2.1314 0.94 2929 163 0.2357 0.3080 REMARK 3 23 2.1314 - 2.1000 0.91 2855 119 0.2510 0.3596 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.270 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.730 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.21 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.92 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.012 5258 REMARK 3 ANGLE : 1.160 7140 REMARK 3 CHIRALITY : 0.058 832 REMARK 3 PLANARITY : 0.008 915 REMARK 3 DIHEDRAL : 13.342 3086 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6E8Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-AUG-18. REMARK 100 THE DEPOSITION ID IS D_1000235793. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-MAR-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL12-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97946 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM 7.2.1 REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37384 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 33.960 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : 0.04700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.19500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 1X0X REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.89 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 200 MM POTASSIUM CHLORIDE, 23% PEG REMARK 280 20000, 0.1 M BIS-TRIS PROPANE PH 7.0, 10 MM NAD; 10 MG/ML, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 287K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 39.39000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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: 7570 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24830 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -39.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 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 MET A 1 REMARK 465 GLY A 46 REMARK 465 GLY A 47 REMARK 465 VAL A 122 REMARK 465 ASP A 123 REMARK 465 GLU A 124 REMARK 465 GLY A 125 REMARK 465 PRO A 126 REMARK 465 ASN A 127 REMARK 465 GLY A 128 REMARK 465 ASN A 293 REMARK 465 MET B 1 REMARK 465 GLY B 121 REMARK 465 VAL B 122 REMARK 465 ASP B 123 REMARK 465 GLU B 124 REMARK 465 GLY B 125 REMARK 465 PRO B 126 REMARK 465 ASN B 127 REMARK 465 LEU B 292 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 ASP A 44 CG OD1 OD2 REMARK 470 ILE A 45 CG1 CG2 CD1 REMARK 470 LYS A 48 CG CD CE NZ REMARK 470 LEU A 50 CG CD1 CD2 REMARK 470 GLU A 59 CG CD OE1 OE2 REMARK 470 VAL A 61 CG1 CG2 REMARK 470 LYS A 68 CG CD CE NZ REMARK 470 ASP A 85 CG OD1 OD2 REMARK 470 LYS A 100 CG CD CE NZ REMARK 470 ARG A 269 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 272 CG CD CE NZ REMARK 470 LYS A 282 CG CD CE NZ REMARK 470 GLU A 285 CG CD OE1 OE2 REMARK 470 LYS A 289 CG CD CE NZ REMARK 470 LEU A 292 CG CD1 CD2 REMARK 470 LYS A 296 CG CD CE NZ REMARK 470 LYS B 48 CG CD CE NZ REMARK 470 LYS B 49 CG CD CE NZ REMARK 470 ASP B 85 CG OD1 OD2 REMARK 470 LYS B 100 CG CD CE NZ REMARK 470 ARG B 139 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 169 CG CD CE NZ REMARK 470 ARG B 269 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 272 CG CD CE NZ REMARK 470 GLU B 285 CG CD OE1 OE2 REMARK 470 GLU B 290 CG CD OE1 OE2 REMARK 470 ASN B 293 CG OD1 ND2 REMARK 470 GLN B 295 CG CD OE1 NE2 REMARK 470 LYS B 296 CG CD CE NZ REMARK 470 LYS B 318 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OE2 GLU A 155 O HOH A 501 2.06 REMARK 500 O CYS A 341 O HOH A 502 2.12 REMARK 500 O HOH B 578 O HOH B 611 2.15 REMARK 500 OE1 GLU A 43 O HOH A 503 2.16 REMARK 500 OE1 GLN B 175 O HOH B 501 2.16 REMARK 500 OE1 GLN A 175 O HOH A 504 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 SER A 11 28.22 -145.92 REMARK 500 LEU A 64 72.03 -115.97 REMARK 500 SER A 283 159.62 -47.25 REMARK 500 SER B 11 32.27 -147.94 REMARK 500 LEU B 64 58.89 -150.56 REMARK 500 LEU B 129 8.45 90.88 REMARK 500 ASN B 344 48.08 -140.25 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 406 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA A 26 O REMARK 620 2 ALA A 27 O 68.9 REMARK 620 3 LEU A 29 O 80.3 99.0 REMARK 620 4 PHE A 32 O 83.1 151.5 80.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K B 404 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA B 26 O REMARK 620 2 ALA B 27 O 75.6 REMARK 620 3 LEU B 29 O 85.5 97.9 REMARK 620 4 PHE B 32 O 77.7 153.3 80.7 REMARK 620 5 HOH B 507 O 109.6 65.3 152.2 124.5 REMARK 620 6 HOH B 584 O 140.9 142.3 95.0 63.9 87.6 REMARK 620 7 HOH B 598 O 133.4 64.5 77.7 139.4 75.0 84.2 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NAD A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NAD B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K B 404 DBREF 6E8Z A 1 349 UNP P21695 GPDA_HUMAN 1 349 DBREF 6E8Z B 1 349 UNP P21695 GPDA_HUMAN 1 349 SEQRES 1 A 349 MET ALA SER LYS LYS VAL CYS ILE VAL GLY SER GLY ASN SEQRES 2 A 349 TRP GLY SER ALA ILE ALA LYS ILE VAL GLY GLY ASN ALA SEQRES 3 A 349 ALA GLN LEU ALA GLN PHE ASP PRO ARG VAL THR MET TRP SEQRES 4 A 349 VAL PHE GLU GLU ASP ILE GLY GLY LYS LYS LEU THR GLU SEQRES 5 A 349 ILE ILE ASN THR GLN HIS GLU ASN VAL LYS TYR LEU PRO SEQRES 6 A 349 GLY HIS LYS LEU PRO PRO ASN VAL VAL ALA VAL PRO ASP SEQRES 7 A 349 VAL VAL GLN ALA ALA GLU ASP ALA ASP ILE LEU ILE PHE SEQRES 8 A 349 VAL VAL PRO HIS GLN PHE ILE GLY LYS ILE CYS ASP GLN SEQRES 9 A 349 LEU LYS GLY HIS LEU LYS ALA ASN ALA THR GLY ILE SER SEQRES 10 A 349 LEU ILE LYS GLY VAL ASP GLU GLY PRO ASN GLY LEU LYS SEQRES 11 A 349 LEU ILE SER GLU VAL ILE GLY GLU ARG LEU GLY ILE PRO SEQRES 12 A 349 MET SER VAL LEU MET GLY ALA ASN ILE ALA SER GLU VAL SEQRES 13 A 349 ALA ASP GLU LYS PHE CYS GLU THR THR ILE GLY CYS LYS SEQRES 14 A 349 ASP PRO ALA GLN GLY GLN LEU LEU LYS GLU LEU MET GLN SEQRES 15 A 349 THR PRO ASN PHE ARG ILE THR VAL VAL GLN GLU VAL ASP SEQRES 16 A 349 THR VAL GLU ILE CYS GLY ALA LEU LYS ASN VAL VAL ALA SEQRES 17 A 349 VAL GLY ALA GLY PHE CYS ASP GLY LEU GLY PHE GLY ASP SEQRES 18 A 349 ASN THR LYS ALA ALA VAL ILE ARG LEU GLY LEU MET GLU SEQRES 19 A 349 MET ILE ALA PHE ALA LYS LEU PHE CYS SER GLY PRO VAL SEQRES 20 A 349 SER SER ALA THR PHE LEU GLU SER CYS GLY VAL ALA ASP SEQRES 21 A 349 LEU ILE THR THR CYS TYR GLY GLY ARG ASN ARG LYS VAL SEQRES 22 A 349 ALA GLU ALA PHE ALA ARG THR GLY LYS SER ILE GLU GLN SEQRES 23 A 349 LEU GLU LYS GLU LEU LEU ASN GLY GLN LYS LEU GLN GLY SEQRES 24 A 349 PRO GLU THR ALA ARG GLU LEU TYR SER ILE LEU GLN HIS SEQRES 25 A 349 LYS GLY LEU VAL ASP LYS PHE PRO LEU PHE MET ALA VAL SEQRES 26 A 349 TYR LYS VAL CYS TYR GLU GLY GLN PRO VAL GLY GLU PHE SEQRES 27 A 349 ILE HIS CYS LEU GLN ASN HIS PRO GLU HIS MET SEQRES 1 B 349 MET ALA SER LYS LYS VAL CYS ILE VAL GLY SER GLY ASN SEQRES 2 B 349 TRP GLY SER ALA ILE ALA LYS ILE VAL GLY GLY ASN ALA SEQRES 3 B 349 ALA GLN LEU ALA GLN PHE ASP PRO ARG VAL THR MET TRP SEQRES 4 B 349 VAL PHE GLU GLU ASP ILE GLY GLY LYS LYS LEU THR GLU SEQRES 5 B 349 ILE ILE ASN THR GLN HIS GLU ASN VAL LYS TYR LEU PRO SEQRES 6 B 349 GLY HIS LYS LEU PRO PRO ASN VAL VAL ALA VAL PRO ASP SEQRES 7 B 349 VAL VAL GLN ALA ALA GLU ASP ALA ASP ILE LEU ILE PHE SEQRES 8 B 349 VAL VAL PRO HIS GLN PHE ILE GLY LYS ILE CYS ASP GLN SEQRES 9 B 349 LEU LYS GLY HIS LEU LYS ALA ASN ALA THR GLY ILE SER SEQRES 10 B 349 LEU ILE LYS GLY VAL ASP GLU GLY PRO ASN GLY LEU LYS SEQRES 11 B 349 LEU ILE SER GLU VAL ILE GLY GLU ARG LEU GLY ILE PRO SEQRES 12 B 349 MET SER VAL LEU MET GLY ALA ASN ILE ALA SER GLU VAL SEQRES 13 B 349 ALA ASP GLU LYS PHE CYS GLU THR THR ILE GLY CYS LYS SEQRES 14 B 349 ASP PRO ALA GLN GLY GLN LEU LEU LYS GLU LEU MET GLN SEQRES 15 B 349 THR PRO ASN PHE ARG ILE THR VAL VAL GLN GLU VAL ASP SEQRES 16 B 349 THR VAL GLU ILE CYS GLY ALA LEU LYS ASN VAL VAL ALA SEQRES 17 B 349 VAL GLY ALA GLY PHE CYS ASP GLY LEU GLY PHE GLY ASP SEQRES 18 B 349 ASN THR LYS ALA ALA VAL ILE ARG LEU GLY LEU MET GLU SEQRES 19 B 349 MET ILE ALA PHE ALA LYS LEU PHE CYS SER GLY PRO VAL SEQRES 20 B 349 SER SER ALA THR PHE LEU GLU SER CYS GLY VAL ALA ASP SEQRES 21 B 349 LEU ILE THR THR CYS TYR GLY GLY ARG ASN ARG LYS VAL SEQRES 22 B 349 ALA GLU ALA PHE ALA ARG THR GLY LYS SER ILE GLU GLN SEQRES 23 B 349 LEU GLU LYS GLU LEU LEU ASN GLY GLN LYS LEU GLN GLY SEQRES 24 B 349 PRO GLU THR ALA ARG GLU LEU TYR SER ILE LEU GLN HIS SEQRES 25 B 349 LYS GLY LEU VAL ASP LYS PHE PRO LEU PHE MET ALA VAL SEQRES 26 B 349 TYR LYS VAL CYS TYR GLU GLY GLN PRO VAL GLY GLU PHE SEQRES 27 B 349 ILE HIS CYS LEU GLN ASN HIS PRO GLU HIS MET HET NAD A 401 70 HET PO4 A 402 5 HET EDO A 403 10 HET EDO A 404 10 HET EDO A 405 10 HET K A 406 1 HET NAD B 401 70 HET PO4 B 402 5 HET EDO B 403 10 HET K B 404 1 HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM PO4 PHOSPHATE ION HETNAM EDO 1,2-ETHANEDIOL HETNAM K POTASSIUM ION HETSYN EDO ETHYLENE GLYCOL FORMUL 3 NAD 2(C21 H27 N7 O14 P2) FORMUL 4 PO4 2(O4 P 3-) FORMUL 5 EDO 4(C2 H6 O2) FORMUL 8 K 2(K 1+) FORMUL 13 HOH *230(H2 O) HELIX 1 AA1 GLY A 12 LEU A 29 1 18 HELIX 2 AA2 LYS A 49 HIS A 58 1 10 HELIX 3 AA3 ASP A 78 GLU A 84 1 7 HELIX 4 AA4 PRO A 94 GLN A 96 5 3 HELIX 5 AA5 PHE A 97 LYS A 106 1 10 HELIX 6 AA6 LEU A 131 GLY A 141 1 11 HELIX 7 AA7 ILE A 152 ASP A 158 1 7 HELIX 8 AA8 ASP A 170 GLN A 182 1 13 HELIX 9 AA9 GLU A 193 GLY A 218 1 26 HELIX 10 AB1 GLY A 220 CYS A 243 1 24 HELIX 11 AB2 SER A 248 GLU A 254 5 7 HELIX 12 AB3 GLY A 257 GLY A 268 1 12 HELIX 13 AB4 GLY A 268 GLY A 281 1 14 HELIX 14 AB5 SER A 283 LEU A 292 1 10 HELIX 15 AB6 LEU A 297 GLY A 314 1 18 HELIX 16 AB7 LEU A 315 LYS A 318 5 4 HELIX 17 AB8 PHE A 319 GLU A 331 1 13 HELIX 18 AB9 PRO A 334 GLN A 343 5 10 HELIX 19 AC1 HIS A 345 MET A 349 5 5 HELIX 20 AC2 GLY B 12 LEU B 29 1 18 HELIX 21 AC3 LYS B 49 HIS B 58 1 10 HELIX 22 AC4 ASP B 78 GLU B 84 1 7 HELIX 23 AC5 PRO B 94 GLN B 96 5 3 HELIX 24 AC6 PHE B 97 LYS B 106 1 10 HELIX 25 AC7 LEU B 131 GLY B 141 1 11 HELIX 26 AC8 ILE B 152 ASP B 158 1 7 HELIX 27 AC9 ASP B 170 GLN B 182 1 13 HELIX 28 AD1 GLU B 193 LEU B 217 1 25 HELIX 29 AD2 GLY B 220 CYS B 243 1 24 HELIX 30 AD3 SER B 248 GLU B 254 5 7 HELIX 31 AD4 GLY B 257 GLY B 268 1 12 HELIX 32 AD5 GLY B 268 GLY B 281 1 14 HELIX 33 AD6 SER B 283 LEU B 291 1 9 HELIX 34 AD7 LEU B 297 LYS B 313 1 17 HELIX 35 AD8 GLY B 314 LYS B 318 5 5 HELIX 36 AD9 PHE B 319 GLU B 331 1 13 HELIX 37 AE1 PRO B 334 PHE B 338 5 5 HELIX 38 AE2 ILE B 339 GLN B 343 5 5 HELIX 39 AE3 HIS B 345 MET B 349 5 5 SHEET 1 AA1 8 VAL A 73 VAL A 76 0 SHEET 2 AA1 8 PHE A 32 TRP A 39 1 N VAL A 36 O VAL A 74 SHEET 3 AA1 8 LYS A 4 VAL A 9 1 N LYS A 4 O ASP A 33 SHEET 4 AA1 8 ILE A 88 PHE A 91 1 O ILE A 90 N VAL A 9 SHEET 5 AA1 8 THR A 114 SER A 117 1 O ILE A 116 N PHE A 91 SHEET 6 AA1 8 MET A 144 MET A 148 1 O SER A 145 N SER A 117 SHEET 7 AA1 8 CYS A 162 GLY A 167 -1 O GLY A 167 N VAL A 146 SHEET 8 AA1 8 PHE A 186 VAL A 191 1 O THR A 189 N ILE A 166 SHEET 1 AA2 8 VAL B 73 VAL B 76 0 SHEET 2 AA2 8 PHE B 32 TRP B 39 1 N VAL B 36 O VAL B 74 SHEET 3 AA2 8 LYS B 4 VAL B 9 1 N LYS B 4 O ASP B 33 SHEET 4 AA2 8 ILE B 88 PHE B 91 1 O ILE B 88 N CYS B 7 SHEET 5 AA2 8 THR B 114 SER B 117 1 O ILE B 116 N PHE B 91 SHEET 6 AA2 8 MET B 144 MET B 148 1 O SER B 145 N SER B 117 SHEET 7 AA2 8 CYS B 162 GLY B 167 -1 O THR B 165 N MET B 148 SHEET 8 AA2 8 PHE B 186 VAL B 191 1 O VAL B 191 N ILE B 166 LINK O ALA A 26 K K A 406 1555 1555 2.64 LINK O ALA A 27 K K A 406 1555 1555 3.18 LINK O LEU A 29 K K A 406 1555 1555 2.64 LINK O PHE A 32 K K A 406 1555 1555 2.77 LINK O ALA B 26 K K B 404 1555 1555 2.73 LINK O ALA B 27 K K B 404 1555 1555 3.02 LINK O LEU B 29 K K B 404 1555 1555 2.50 LINK O PHE B 32 K K B 404 1555 1555 2.65 LINK K K B 404 O HOH B 507 1555 1655 2.86 LINK K K B 404 O HOH B 584 1555 1555 2.83 LINK K K B 404 O HOH B 598 1555 1555 3.41 SITE 1 AC1 20 SER A 11 GLY A 12 ASN A 13 TRP A 14 SITE 2 AC1 20 TRP A 39 PHE A 41 VAL A 93 PRO A 94 SITE 3 AC1 20 PHE A 97 ILE A 119 LYS A 120 ASN A 151 SITE 4 AC1 20 ILE A 152 ALA A 153 HOH A 505 HOH A 527 SITE 5 AC1 20 HOH A 538 HOH A 547 HOH A 553 HOH A 554 SITE 1 AC2 5 LEU A 131 GLU A 134 ASP A 195 PHE A 242 SITE 2 AC2 5 SER A 244 SITE 1 AC3 4 ALA A 237 LYS A 318 PRO A 346 GLU A 347 SITE 1 AC4 4 LYS A 240 PRO A 246 VAL A 247 HOH A 511 SITE 1 AC5 7 LYS A 120 GLY A 149 ASN A 151 LYS A 204 SITE 2 AC5 7 ASP A 260 THR A 263 THR A 264 SITE 1 AC6 6 ALA A 26 ALA A 27 LEU A 29 PHE A 32 SITE 2 AC6 6 PRO A 34 ASN A 344 SITE 1 AC7 21 SER B 11 GLY B 12 ASN B 13 TRP B 14 SITE 2 AC7 21 TRP B 39 PHE B 41 TYR B 63 VAL B 93 SITE 3 AC7 21 PRO B 94 PHE B 97 ILE B 119 LYS B 120 SITE 4 AC7 21 ASN B 151 ILE B 152 ALA B 153 HOH B 505 SITE 5 AC7 21 HOH B 511 HOH B 517 HOH B 533 HOH B 545 SITE 6 AC7 21 HOH B 586 SITE 1 AC8 4 GLU B 134 ASP B 195 PHE B 242 SER B 244 SITE 1 AC9 4 LYS B 318 HIS B 345 PRO B 346 GLU B 347 SITE 1 AD1 6 ALA B 26 ALA B 27 LEU B 29 PHE B 32 SITE 2 AD1 6 HOH B 507 HOH B 584 CRYST1 63.580 78.780 69.179 90.00 104.32 90.00 P 1 21 1 4 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 0.015728 0.000000 0.004015 0.00000 SCALE2 0.000000 0.012694 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014919 0.00000