HEADER OXIDOREDUCTASE/INHIBITOR 30-JUN-19 6PLF TITLE CRYSTAL STRUCTURE OF HUMAN PHGDH COMPLEXED WITH COMPOUND 1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: D-3-PHOSPHOGLYCERATE DEHYDROGENASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: 3-PGDH,2-OXOGLUTARATE REDUCTASE,MALATE DEHYDROGENASE; COMPND 5 EC: 1.1.1.95,1.1.1.399,1.1.1.37; 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: PHGDH, PGDH3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS DEHYDROGENASE, SERINE METABOLISM, OXIDOREDUCTASE, OXIDOREDUCTASE- KEYWDS 2 INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.OLLAND,D.LAKSHMINARASIMHAN,A.WHITE,R.K.SUTO REVDAT 4 13-MAR-24 6PLF 1 REMARK REVDAT 3 04-SEP-19 6PLF 1 JRNL REVDAT 2 07-AUG-19 6PLF 1 JRNL REVDAT 1 24-JUL-19 6PLF 0 JRNL AUTH E.MULLARKY,J.XU,A.D.ROBIN,D.J.HUGGINS,A.JENNINGS,N.NOGUCHI, JRNL AUTH 2 A.OLLAND,D.LAKSHMINARASIMHAN,M.MILLER,D.TOMITA,M.MICHINO, JRNL AUTH 3 T.SU,G.ZHANG,A.W.STAMFORD,P.T.MEINKE,S.KARGMAN,L.C.CANTLEY JRNL TITL INHIBITION OF 3-PHOSPHOGLYCERATE DEHYDROGENASE (PHGDH) BY JRNL TITL 2 INDOLE AMIDES ABROGATES DE NOVO SERINE SYNTHESIS IN CANCER JRNL TITL 3 CELLS. JRNL REF BIOORG.MED.CHEM.LETT. V. 29 2503 2019 JRNL REFN ESSN 1464-3405 JRNL PMID 31327531 JRNL DOI 10.1016/J.BMCL.2019.07.011 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0238 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.37 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.8 REMARK 3 NUMBER OF REFLECTIONS : 62907 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) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3288 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4508 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.45 REMARK 3 BIN R VALUE (WORKING SET) : 0.3030 REMARK 3 BIN FREE R VALUE SET COUNT : 230 REMARK 3 BIN FREE R VALUE : 0.3220 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4349 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 86 REMARK 3 SOLVENT ATOMS : 283 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.49 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.92000 REMARK 3 B22 (A**2) : 4.22000 REMARK 3 B33 (A**2) : -2.11000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.19000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.107 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.108 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.092 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.989 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.962 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.944 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4586 ; 0.010 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 4332 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6221 ; 1.700 ; 1.660 REMARK 3 BOND ANGLES OTHERS (DEGREES): 10031 ; 1.399 ; 1.584 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 617 ; 7.393 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 205 ;35.528 ;22.293 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 773 ;16.175 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 33 ;17.859 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 627 ; 0.086 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5231 ; 0.009 ; 0.023 REMARK 3 GENERAL PLANES OTHERS (A): 882 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 6PLF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-JUL-19. REMARK 100 THE DEPOSITION ID IS D_1000242629. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-NOV-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.07822 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 66230 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 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 (%) : 96.0 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : 0.56800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.28 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS PH 5.5 AND A RANGE OF REMARK 280 PEG 3350 (24% TO 29%), USING MICRO-SEEDING, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 297K 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 63.09600 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: 6040 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24650 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 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 SER A 2 REMARK 465 MET A 3 REMARK 465 ALA A 4 REMARK 465 LYS A 310 REMARK 465 SER A 311 REMARK 465 LEU A 312 REMARK 465 THR A 313 REMARK 465 GLY A 314 REMARK 465 VAL A 315 REMARK 465 SER B 2 REMARK 465 MET B 3 REMARK 465 ALA B 4 REMARK 465 ASN B 5 REMARK 465 LEU B 6 REMARK 465 SER B 37 REMARK 465 LYS B 38 REMARK 465 GLU B 39 REMARK 465 GLU B 40 REMARK 465 THR B 57 REMARK 465 LYS B 58 REMARK 465 VAL B 59 REMARK 465 THR B 60 REMARK 465 VAL B 307 REMARK 465 LYS B 308 REMARK 465 GLY B 309 REMARK 465 LYS B 310 REMARK 465 SER B 311 REMARK 465 LEU B 312 REMARK 465 THR B 313 REMARK 465 GLY B 314 REMARK 465 VAL B 315 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 LEU A 6 CG CD1 CD2 REMARK 470 LYS A 21 CG CD CE NZ REMARK 470 LYS A 33 CG CD CE NZ REMARK 470 LYS A 136 CG CD CE NZ REMARK 470 LYS B 8 CG CD CE NZ REMARK 470 LEU B 10 CG CD1 CD2 REMARK 470 ASP B 13 CG OD1 OD2 REMARK 470 LEU B 15 CG CD1 CD2 REMARK 470 LYS B 21 CG CD CE NZ REMARK 470 LEU B 23 CG CD1 CD2 REMARK 470 LEU B 28 CG CD1 CD2 REMARK 470 GLN B 29 CG CD OE1 NE2 REMARK 470 GLU B 32 CG CD OE1 OE2 REMARK 470 LYS B 33 CG CD CE NZ REMARK 470 GLN B 34 CG CD OE1 NE2 REMARK 470 LEU B 41 CG CD1 CD2 REMARK 470 ILE B 42 CG1 CG2 CD1 REMARK 470 GLU B 44 CG CD OE1 OE2 REMARK 470 LEU B 45 CG CD1 CD2 REMARK 470 GLN B 46 CG CD OE1 NE2 REMARK 470 ASP B 47 CG OD1 OD2 REMARK 470 GLU B 49 CG CD OE1 OE2 REMARK 470 ARG B 54 CG CD NE CZ NH1 NH2 REMARK 470 ASP B 62 CG OD1 OD2 REMARK 470 ILE B 64 CG1 CG2 CD1 REMARK 470 GLU B 68 CG CD OE1 OE2 REMARK 470 LYS B 69 CG CD CE NZ REMARK 470 ASP B 81 CG OD1 OD2 REMARK 470 ARG B 90 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 91 CG CD CE NZ REMARK 470 ASP B 305 CG OD1 OD2 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 O ASP A 175 O HOH A 501 2.11 REMARK 500 O ASP B 175 O HOH B 501 2.16 REMARK 500 NH2 ARG B 294 O HOH B 502 2.18 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 LYS A 8 129.73 62.57 REMARK 500 PRO A 17 -5.22 -57.35 REMARK 500 ASN A 35 -91.85 59.38 REMARK 500 LEU A 36 119.43 64.87 REMARK 500 ARG A 54 -109.97 -104.68 REMARK 500 ARG A 54 -109.92 -104.68 REMARK 500 VAL A 59 79.07 -111.51 REMARK 500 GLU A 68 40.31 -106.13 REMARK 500 LYS A 69 -40.45 -148.92 REMARK 500 LEU A 70 118.76 -32.43 REMARK 500 ASP A 84 90.83 -65.30 REMARK 500 GLU A 134 53.69 -112.76 REMARK 500 HIS A 206 48.08 -143.22 REMARK 500 ALA A 235 -82.27 -105.84 REMARK 500 LYS A 308 38.66 -85.53 REMARK 500 SER B 12 40.34 -80.18 REMARK 500 SER B 14 93.38 -51.59 REMARK 500 PRO B 17 -17.68 -49.32 REMARK 500 LEU B 23 48.08 -70.10 REMARK 500 GLN B 24 23.59 -141.94 REMARK 500 LEU B 28 85.31 -157.02 REMARK 500 VAL B 31 96.23 -164.31 REMARK 500 GLN B 46 -84.79 -68.94 REMARK 500 ARG B 54 -86.87 -109.77 REMARK 500 LYS B 69 89.30 -21.48 REMARK 500 GLN B 71 -73.18 -91.08 REMARK 500 VAL B 80 26.30 -148.61 REMARK 500 ASP B 81 29.34 -73.29 REMARK 500 ASN B 82 19.66 -146.03 REMARK 500 GLU B 134 71.44 -105.95 REMARK 500 HIS B 206 52.19 -140.06 REMARK 500 ALA B 235 -81.46 -106.54 REMARK 500 PHE B 303 -70.15 -62.74 REMARK 500 VAL B 304 2.03 -69.25 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ASP B 25 GLY B 26 -146.68 REMARK 500 GLY B 92 ILE B 93 -149.26 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 A 638 DISTANCE = 5.82 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ONV A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO 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 ONV B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 403 DBREF 6PLF A 4 315 UNP O43175 SERA_HUMAN 4 315 DBREF 6PLF B 4 315 UNP O43175 SERA_HUMAN 4 315 SEQADV 6PLF SER A 2 UNP O43175 EXPRESSION TAG SEQADV 6PLF MET A 3 UNP O43175 EXPRESSION TAG SEQADV 6PLF SER B 2 UNP O43175 EXPRESSION TAG SEQADV 6PLF MET B 3 UNP O43175 EXPRESSION TAG SEQRES 1 A 314 SER MET ALA ASN LEU ARG LYS VAL LEU ILE SER ASP SER SEQRES 2 A 314 LEU ASP PRO CYS CYS ARG LYS ILE LEU GLN ASP GLY GLY SEQRES 3 A 314 LEU GLN VAL VAL GLU LYS GLN ASN LEU SER LYS GLU GLU SEQRES 4 A 314 LEU ILE ALA GLU LEU GLN ASP CYS GLU GLY LEU ILE VAL SEQRES 5 A 314 ARG SER ALA THR LYS VAL THR ALA ASP VAL ILE ASN ALA SEQRES 6 A 314 ALA GLU LYS LEU GLN VAL VAL GLY ARG ALA GLY THR GLY SEQRES 7 A 314 VAL ASP ASN VAL ASP LEU GLU ALA ALA THR ARG LYS GLY SEQRES 8 A 314 ILE LEU VAL MET ASN THR PRO ASN GLY ASN SER LEU SER SEQRES 9 A 314 ALA ALA GLU LEU THR CYS GLY MET ILE MET CYS LEU ALA SEQRES 10 A 314 ARG GLN ILE PRO GLN ALA THR ALA SER MET LYS ASP GLY SEQRES 11 A 314 LYS TRP GLU ARG LYS LYS PHE MET GLY THR GLU LEU ASN SEQRES 12 A 314 GLY LYS THR LEU GLY ILE LEU GLY LEU GLY ARG ILE GLY SEQRES 13 A 314 ARG GLU VAL ALA THR ARG MET GLN SER PHE GLY MET LYS SEQRES 14 A 314 THR ILE GLY TYR ASP PRO ILE ILE SER PRO GLU VAL SER SEQRES 15 A 314 ALA SER PHE GLY VAL GLN GLN LEU PRO LEU GLU GLU ILE SEQRES 16 A 314 TRP PRO LEU CYS ASP PHE ILE THR VAL HIS THR PRO LEU SEQRES 17 A 314 LEU PRO SER THR THR GLY LEU LEU ASN ASP ASN THR PHE SEQRES 18 A 314 ALA GLN CYS LYS LYS GLY VAL ARG VAL VAL ASN CYS ALA SEQRES 19 A 314 ARG GLY GLY ILE VAL ASP GLU GLY ALA LEU LEU ARG ALA SEQRES 20 A 314 LEU GLN SER GLY GLN CYS ALA GLY ALA ALA LEU ASP VAL SEQRES 21 A 314 PHE THR GLU GLU PRO PRO ARG ASP ARG ALA LEU VAL ASP SEQRES 22 A 314 HIS GLU ASN VAL ILE SER CYS PRO HIS LEU GLY ALA SER SEQRES 23 A 314 THR LYS GLU ALA GLN SER ARG CYS GLY GLU GLU ILE ALA SEQRES 24 A 314 VAL GLN PHE VAL ASP MET VAL LYS GLY LYS SER LEU THR SEQRES 25 A 314 GLY VAL SEQRES 1 B 314 SER MET ALA ASN LEU ARG LYS VAL LEU ILE SER ASP SER SEQRES 2 B 314 LEU ASP PRO CYS CYS ARG LYS ILE LEU GLN ASP GLY GLY SEQRES 3 B 314 LEU GLN VAL VAL GLU LYS GLN ASN LEU SER LYS GLU GLU SEQRES 4 B 314 LEU ILE ALA GLU LEU GLN ASP CYS GLU GLY LEU ILE VAL SEQRES 5 B 314 ARG SER ALA THR LYS VAL THR ALA ASP VAL ILE ASN ALA SEQRES 6 B 314 ALA GLU LYS LEU GLN VAL VAL GLY ARG ALA GLY THR GLY SEQRES 7 B 314 VAL ASP ASN VAL ASP LEU GLU ALA ALA THR ARG LYS GLY SEQRES 8 B 314 ILE LEU VAL MET ASN THR PRO ASN GLY ASN SER LEU SER SEQRES 9 B 314 ALA ALA GLU LEU THR CYS GLY MET ILE MET CYS LEU ALA SEQRES 10 B 314 ARG GLN ILE PRO GLN ALA THR ALA SER MET LYS ASP GLY SEQRES 11 B 314 LYS TRP GLU ARG LYS LYS PHE MET GLY THR GLU LEU ASN SEQRES 12 B 314 GLY LYS THR LEU GLY ILE LEU GLY LEU GLY ARG ILE GLY SEQRES 13 B 314 ARG GLU VAL ALA THR ARG MET GLN SER PHE GLY MET LYS SEQRES 14 B 314 THR ILE GLY TYR ASP PRO ILE ILE SER PRO GLU VAL SER SEQRES 15 B 314 ALA SER PHE GLY VAL GLN GLN LEU PRO LEU GLU GLU ILE SEQRES 16 B 314 TRP PRO LEU CYS ASP PHE ILE THR VAL HIS THR PRO LEU SEQRES 17 B 314 LEU PRO SER THR THR GLY LEU LEU ASN ASP ASN THR PHE SEQRES 18 B 314 ALA GLN CYS LYS LYS GLY VAL ARG VAL VAL ASN CYS ALA SEQRES 19 B 314 ARG GLY GLY ILE VAL ASP GLU GLY ALA LEU LEU ARG ALA SEQRES 20 B 314 LEU GLN SER GLY GLN CYS ALA GLY ALA ALA LEU ASP VAL SEQRES 21 B 314 PHE THR GLU GLU PRO PRO ARG ASP ARG ALA LEU VAL ASP SEQRES 22 B 314 HIS GLU ASN VAL ILE SER CYS PRO HIS LEU GLY ALA SER SEQRES 23 B 314 THR LYS GLU ALA GLN SER ARG CYS GLY GLU GLU ILE ALA SEQRES 24 B 314 VAL GLN PHE VAL ASP MET VAL LYS GLY LYS SER LEU THR SEQRES 25 B 314 GLY VAL HET ONV A 401 33 HET EDO A 402 4 HET EDO A 403 4 HET EDO A 404 4 HET ONV B 401 33 HET EDO B 402 4 HET EDO B 403 4 HETNAM ONV 4-{(1S)-1-[(5-CHLORO-6-{[(5S)-2-OXO-1,3-OXAZOLIDIN-5- HETNAM 2 ONV YL]METHOXY}-1H-INDOLE-2-CARBONYL)AMINO]-2- HETNAM 3 ONV HYDROXYETHYL}BENZOIC ACID HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 ONV 2(C22 H20 CL N3 O7) FORMUL 4 EDO 5(C2 H6 O2) FORMUL 10 HOH *283(H2 O) HELIX 1 AA1 PRO A 17 GLY A 26 1 10 HELIX 2 AA2 SER A 37 LEU A 45 1 9 HELIX 3 AA3 GLN A 46 CYS A 48 5 3 HELIX 4 AA4 THR A 60 ALA A 67 1 8 HELIX 5 AA5 ASP A 84 LYS A 91 1 8 HELIX 6 AA6 THR A 98 GLY A 101 5 4 HELIX 7 AA7 ASN A 102 GLN A 120 1 19 HELIX 8 AA8 GLN A 120 ASP A 130 1 11 HELIX 9 AA9 GLY A 154 SER A 166 1 13 HELIX 10 AB1 SER A 179 SER A 185 1 7 HELIX 11 AB2 PRO A 192 TRP A 197 1 6 HELIX 12 AB3 PRO A 198 CYS A 200 5 3 HELIX 13 AB4 LEU A 210 THR A 214 5 5 HELIX 14 AB5 ASN A 218 CYS A 225 1 8 HELIX 15 AB6 ASP A 241 GLY A 252 1 12 HELIX 16 AB7 ARG A 270 HIS A 275 1 6 HELIX 17 AB8 THR A 288 LYS A 308 1 21 HELIX 18 AB9 PRO B 17 LEU B 23 1 7 HELIX 19 AC1 ASP B 62 ALA B 67 1 6 HELIX 20 AC2 ASP B 84 LYS B 91 1 8 HELIX 21 AC3 ASN B 102 GLN B 120 1 19 HELIX 22 AC4 GLN B 120 ASP B 130 1 11 HELIX 23 AC5 GLY B 154 SER B 166 1 13 HELIX 24 AC6 SER B 179 SER B 185 1 7 HELIX 25 AC7 PRO B 192 TRP B 197 1 6 HELIX 26 AC8 PRO B 198 CYS B 200 5 3 HELIX 27 AC9 LEU B 210 THR B 214 5 5 HELIX 28 AD1 ASN B 218 CYS B 225 1 8 HELIX 29 AD2 ASP B 241 GLY B 252 1 12 HELIX 30 AD3 THR B 288 VAL B 304 1 17 SHEET 1 AA1 5 VAL A 30 GLU A 32 0 SHEET 2 AA1 5 VAL A 9 ILE A 11 1 N VAL A 9 O VAL A 31 SHEET 3 AA1 5 GLY A 50 VAL A 53 1 O GLY A 50 N LEU A 10 SHEET 4 AA1 5 VAL A 72 ARG A 75 1 O GLY A 74 N VAL A 53 SHEET 5 AA1 5 LEU A 94 MET A 96 1 O LEU A 94 N VAL A 73 SHEET 1 AA2 7 VAL A 188 GLN A 190 0 SHEET 2 AA2 7 LYS A 170 TYR A 174 1 N GLY A 173 O GLN A 189 SHEET 3 AA2 7 THR A 147 LEU A 151 1 N LEU A 148 O LYS A 170 SHEET 4 AA2 7 PHE A 202 VAL A 205 1 O THR A 204 N GLY A 149 SHEET 5 AA2 7 ARG A 230 ASN A 233 1 O VAL A 232 N ILE A 203 SHEET 6 AA2 7 GLY A 256 LEU A 259 1 O ALA A 258 N ASN A 233 SHEET 7 AA2 7 VAL A 278 SER A 280 1 O ILE A 279 N ALA A 257 SHEET 1 AA3 3 LEU B 51 VAL B 53 0 SHEET 2 AA3 3 VAL B 72 ARG B 75 1 O VAL B 72 N LEU B 51 SHEET 3 AA3 3 LEU B 94 ASN B 97 1 O MET B 96 N VAL B 73 SHEET 1 AA4 7 VAL B 188 GLN B 190 0 SHEET 2 AA4 7 LYS B 170 TYR B 174 1 N GLY B 173 O GLN B 189 SHEET 3 AA4 7 THR B 147 LEU B 151 1 N LEU B 148 O LYS B 170 SHEET 4 AA4 7 PHE B 202 VAL B 205 1 O PHE B 202 N GLY B 149 SHEET 5 AA4 7 ARG B 230 ASN B 233 1 O VAL B 232 N ILE B 203 SHEET 6 AA4 7 GLY B 256 LEU B 259 1 O ALA B 258 N ASN B 233 SHEET 7 AA4 7 VAL B 278 SER B 280 1 O ILE B 279 N LEU B 259 CISPEP 1 GLU A 265 PRO A 266 0 -12.04 CISPEP 2 GLU B 265 PRO B 266 0 -4.26 SITE 1 AC1 15 TYR A 174 ASP A 175 PRO A 176 ILE A 178 SITE 2 AC1 15 HIS A 206 THR A 207 PRO A 208 SER A 212 SITE 3 AC1 15 THR A 213 LEU A 216 HOH A 505 HOH A 529 SITE 4 AC1 15 HOH A 531 HOH A 579 GLU B 194 SITE 1 AC2 7 GLU A 242 PHE A 262 ASP A 269 ARG A 270 SITE 2 AC2 7 LEU A 272 VAL A 273 HOH A 509 SITE 1 AC3 7 LYS A 170 THR A 171 GLY A 187 GLN A 189 SITE 2 AC3 7 HOH A 562 HOH A 573 ASP B 130 SITE 1 AC4 7 LEU A 117 GLN A 120 GLN A 123 ARG A 230 SITE 2 AC4 7 ALA A 255 HOH A 502 HOH A 533 SITE 1 AC5 16 GLU A 194 HOH A 529 ARG B 155 TYR B 174 SITE 2 AC5 16 ASP B 175 PRO B 176 ILE B 177 ILE B 178 SITE 3 AC5 16 LEU B 193 HIS B 206 THR B 207 PRO B 208 SITE 4 AC5 16 SER B 212 THR B 213 LEU B 216 HOH B 509 SITE 1 AC6 7 GLU B 242 PRO B 267 ASP B 269 ARG B 270 SITE 2 AC6 7 LEU B 272 VAL B 273 HOH B 599 SITE 1 AC7 6 LEU B 117 GLN B 120 GLN B 123 ARG B 230 SITE 2 AC7 6 ALA B 255 ASN B 277 CRYST1 43.202 126.192 59.504 90.00 99.76 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 0.023147 0.000000 0.003983 0.00000 SCALE2 0.000000 0.007924 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017053 0.00000