10 20 30 40 50 60 70 80 3H82 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER TRANSCRIPTION 28-APR-09 3H82
TITLE CRYSTAL STRUCTURE OF THE HIGH AFFINITY HETERODIMER OF HIF2 TITLE 2 ALPHA AND ARNT C-TERMINAL PAS DOMAINS WITH THE ARTIFICIAL TITLE 3 LIGAND THS020
COMPND MOL_ID: 1; COMPND 2 MOLECULE: ARYL HYDROCARBON RECEPTOR NUCLEAR TRANSLOCATOR; COMPND 3 CHAIN: B; COMPND 4 FRAGMENT: ARNT C-TERMINAL PAS DOMAIN (UNP RESIDUES 356 TO COMPND 5 470); COMPND 6 SYNONYM: ARNT PROTEIN, CLASS E BASIC HELIX-LOOP-HELIX COMPND 7 PROTEIN 2, BHLHE2, DIOXIN RECEPTOR, NUCLEAR TRANSLOCATOR, COMPND 8 HYPOXIA-INDUCIBLE FACTOR 1 BETA, HIF-1 BETA; COMPND 9 ENGINEERED: YES; COMPND 10 MUTATION: YES; COMPND 11 MOL_ID: 2; COMPND 12 MOLECULE: ENDOTHELIAL PAS DOMAIN-CONTAINING PROTEIN 1; COMPND 13 CHAIN: A; COMPND 14 FRAGMENT: HIF2ALPHA C-TERMINAL PAS DOMAIN (UNP RESIDUES 239 COMPND 15 TO 350); COMPND 16 SYNONYM: EPAS-1, MEMBER OF PAS PROTEIN 2, BASIC-HELIX-LOOP- COMPND 17 HELIX-PAS PROTEIN MOP2, HYPOXIA-INDUCIBLE FACTOR 2 ALPHA, COMPND 18 HIF-2 ALPHA, HIF2 ALPHA, HIF-1 ALPHA-LIKE FACTOR, HLF; COMPND 19 ENGINEERED: YES; COMPND 20 MUTATION: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: ARNT, ARYL HYDROCARBON RECEPTOR NUCLEAR TRANSLOCATOR, SOURCE 6 BHLHE2; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PHIS-GB1-ARNT-PAS-B; SOURCE 12 MOL_ID: 2; SOURCE 13 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 14 ORGANISM_COMMON: HUMAN; SOURCE 15 ORGANISM_TAXID: 9606; SOURCE 16 GENE: EPAS1, HIF2A, HYPOXIA INDUCIBLE FACTOR 2 ALPHA, MOP2; SOURCE 17 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 18 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 19 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 20 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 21 EXPRESSION_SYSTEM_PLASMID: PHIS-GB1-HIF2APAS-B
KEYWDS PAS DOMAIN, HETERODIMER, PROTEIN LIGAND COMPLEX., ACTIVATOR, KEYWDS 2 ANGIOGENESIS, CONGENITAL ERYTHROCYTOSIS, DEVELOPMENTAL KEYWDS 3 PROTEIN, DIFFERENTIATION, DISEASE MUTATION, DNA-BINDING, KEYWDS 4 HYDROXYLATION, NUCLEUS, PHOSPHOPROTEIN, TRANSCRIPTION, KEYWDS 5 TRANSCRIPTION REGULATION, UBL CONJUGATION, ALTERNATIVE KEYWDS 6 SPLICING, POLYMORPHISM
EXPDTA X-RAY DIFFRACTION
AUTHOR J.M.KEY,T.H.SCHEUERMANN,P.C.ANDERSON,V.DAGGETT,K.H.GARDNER
REVDAT 1 12-JAN-10 3H82 0
JRNL AUTH J.KEY,T.H.SCHEUERMANN,P.C.ANDERSON,V.DAGGETT, JRNL AUTH 2 K.H.GARDNER JRNL TITL PRINCIPLES OF LIGAND BINDING WITHIN A COMPLETELY JRNL TITL 2 BURIED CAVITY IN HIF2ALPHA PAS-B JRNL REF J.AM.CHEM.SOC. V. 131 17647 2009 JRNL REFN ISSN 0002-7863 JRNL PMID 19950993 JRNL DOI 10.1021/JA9073062
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.44 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 94.6 REMARK 3 NUMBER OF REFLECTIONS : 34380 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) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1710 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) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.53 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1764 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 68.80 REMARK 3 BIN R VALUE (WORKING SET) : 0.2970 REMARK 3 BIN FREE R VALUE SET COUNT : 96 REMARK 3 BIN FREE R VALUE : 0.4090 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1993 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 20 REMARK 3 SOLVENT ATOMS : 215 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.092 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.094 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.064 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.686 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.960 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): 2038 ; 0.019 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2773 ; 1.833 ; 1.942 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 253 ; 6.639 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 101 ;37.755 ;24.158 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 353 ;12.534 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;18.260 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 294 ; 0.141 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1591 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 931 ; 0.244 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1446 ; 0.309 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 160 ; 0.161 ; 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): 47 ; 0.218 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 25 ; 0.108 ; 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): 1246 ; 1.341 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1989 ; 2.071 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 913 ; 2.998 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 784 ; 4.221 ; 4.500 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 : 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: NULL
REMARK 4 REMARK 4 3H82 COMPLIES WITH FORMAT V. 3.20, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-MAY-09. REMARK 100 THE RCSB ID CODE IS RCSB052809.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-DEC-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97915 REMARK 200 MONOCHROMATOR : CUSTOM REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : SBC-2 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34380 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.6 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : 0.04600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 21.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 68.8 REMARK 200 DATA REDUNDANCY IN SHELL : 1.70 REMARK 200 R MERGE FOR SHELL (I) : 0.26900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.480 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: PDB ENTRY 3F1N REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.72 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M BISTRIS, 25% PEG3350, PH 6.0, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
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 35.14000 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 300 REMARK: THE BIOLOGICALLY RELEVANT COMPLEX IS PRESENT IN THE ASU
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: 2040 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11730 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 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 GLY B 350 REMARK 465 GLU B 351 REMARK 465 PHE B 352 REMARK 465 LYS B 353 REMARK 465 GLY B 354 REMARK 465 SER B 468 REMARK 465 GLN B 469 REMARK 465 GLU B 470 REMARK 465 GLY A -2 REMARK 465 ASN A 350
REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LEU B 355 CG CD1 CD2 REMARK 480 GLN B 359 CD OE1 NE2 REMARK 480 SER B 467 CB OG REMARK 480 GLU A -1 CG CD OE1 OE2 REMARK 480 GLU A 263 CD OE1 OE2 REMARK 480 GLU A 270 CG CD OE1 OE2 REMARK 480 LYS A 299 CE NZ REMARK 480 ARG A 330 CG CD NE CZ NH1 NH2 REMARK 480 LYS A 349 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 SD MET A 338 O HOH B 129 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OE2 GLU A -1 O HOH B 211 1655 1.99 REMARK 500 OE1 GLU A -1 O HOH B 131 1655 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 LEU B 355 CB LEU B 355 CG 0.211 REMARK 500 GLN B 359 CG GLN B 359 CD -0.196 REMARK 500 GLU A -1 CB GLU A -1 CG -0.228 REMARK 500 GLY A 2 C LEU A 239 N 0.219 REMARK 500 GLU A 263 CG GLU A 263 CD 0.116 REMARK 500 LYS A 299 CD LYS A 299 CE -0.244 REMARK 500 ARG A 330 CB ARG A 330 CG -0.177 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 GLN B 359 CB - CG - CD ANGL. DEV. = 19.9 DEGREES REMARK 500 GLN B 359 CG - CD - OE1 ANGL. DEV. = -17.4 DEGREES REMARK 500 GLN B 359 CG - CD - NE2 ANGL. DEV. = 16.2 DEGREES REMARK 500 ARG B 362 NE - CZ - NH1 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG B 379 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 SER B 467 CB - CA - C ANGL. DEV. = -26.2 DEGREES REMARK 500 GLU A -1 CA - CB - CG ANGL. DEV. = 15.7 DEGREES REMARK 500 GLU A -1 CB - CG - CD ANGL. DEV. = -19.5 DEGREES REMARK 500 LYS A 299 CG - CD - CE ANGL. DEV. = 28.4 DEGREES 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 MET A 252 6.93 86.14 REMARK 500 ILE A 265 21.66 -150.60 REMARK 500 REMARK 500 REMARK: NULL
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 020 A 351
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3F1P RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A HIGH AFFINITY HETERODIMER OF HIF2 REMARK 900 ALPHA AND ARNT C-TERMINAL PAS DOMAINS. REMARK 900 RELATED ID: 3F1N RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A HIGH AFFINITY HETERODIMER OF HIF2 REMARK 900 ALPHA AND ARNT C-TERMINAL PAS DOMAINS, WITH INTERNALLY REMARK 900 BOUND ETHYLENE GLYCOL. REMARK 900 RELATED ID: 3F1O RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE HIGH AFFINITY HETERODIMER OF HIF2 REMARK 900 ALPHA AND ARNT C-TERMINAL PAS DOMAINS, WITH THE INTERNALLY- REMARK 900 BOUND ARTIFICIAL LIGAND THS-044. REMARK 900 RELATED ID: 2A24 RELATED DB: PDB REMARK 900 NMR-GUIDED MODEL OF THE HETERODIMER OF THE WILD-TYPE HIF2 REMARK 900 ALPHA AND ARNT C-TERMINAL PAS DOMAINS. REMARK 900 RELATED ID: 2B02 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE ARNT C-TERMINAL PAS DOMAIN. REMARK 900 RELATED ID: 1P97 RELATED DB: PDB REMARK 900 NMR STRUCTURE OF THE HIF2 ALPHA C-TERMINAL PAS DOMAIN. REMARK 900 RELATED ID: 1X0O RELATED DB: PDB REMARK 900 NMR STRUCTURE OF THE ARNT C-TERMINAL PAS DOMAIN. REMARK 900 RELATED ID: 3H7W RELATED DB: PDB REMARK 900 HETERODIMER OF HIF2 ALPHA AND ARNT C-TERMINAL PAS DOMAINS REMARK 900 WITH THE ARTIFICIAL LIGAND THS017
DBREF 3H82 B 356 470 UNP P27540 ARNT_HUMAN 356 470 DBREF 3H82 A 239 350 UNP Q99814 EPAS1_HUMAN 239 350
SEQADV 3H82 GLY B 350 UNP P27540 EXPRESSION TAG SEQADV 3H82 GLU B 351 UNP P27540 EXPRESSION TAG SEQADV 3H82 PHE B 352 UNP P27540 EXPRESSION TAG SEQADV 3H82 LYS B 353 UNP P27540 EXPRESSION TAG SEQADV 3H82 GLY B 354 UNP P27540 EXPRESSION TAG SEQADV 3H82 LEU B 355 UNP P27540 EXPRESSION TAG SEQADV 3H82 ARG B 362 UNP P27540 GLU 362 ENGINEERED SEQADV 3H82 GLY A -2 UNP Q99814 EXPRESSION TAG SEQADV 3H82 GLU A -1 UNP Q99814 EXPRESSION TAG SEQADV 3H82 PHE A 0 UNP Q99814 EXPRESSION TAG SEQADV 3H82 LYS A 1 UNP Q99814 EXPRESSION TAG SEQADV 3H82 GLY A 2 UNP Q99814 EXPRESSION TAG SEQADV 3H82 GLU A 247 UNP Q99814 ARG 247 ENGINEERED
SEQRES 1 B 121 GLY GLU PHE LYS GLY LEU ASN VAL CYS GLN PRO THR ARG SEQRES 2 B 121 PHE ILE SER ARG HIS ASN ILE GLU GLY ILE PHE THR PHE SEQRES 3 B 121 VAL ASP HIS ARG CYS VAL ALA THR VAL GLY TYR GLN PRO SEQRES 4 B 121 GLN GLU LEU LEU GLY LYS ASN ILE VAL GLU PHE CYS HIS SEQRES 5 B 121 PRO GLU ASP GLN GLN LEU LEU ARG ASP SER PHE GLN GLN SEQRES 6 B 121 VAL VAL LYS LEU LYS GLY GLN VAL LEU SER VAL MET PHE SEQRES 7 B 121 ARG PHE ARG SER LYS ASN GLN GLU TRP LEU TRP MET ARG SEQRES 8 B 121 THR SER SER PHE THR PHE GLN ASN PRO TYR SER ASP GLU SEQRES 9 B 121 ILE GLU TYR ILE ILE CYS THR ASN THR ASN VAL LYS ASN SEQRES 10 B 121 SER SER GLN GLU SEQRES 1 A 117 GLY GLU PHE LYS GLY LEU ASP SER LYS THR PHE LEU SER SEQRES 2 A 117 GLU HIS SER MET ASP MET LYS PHE THR TYR CYS ASP ASP SEQRES 3 A 117 ARG ILE THR GLU LEU ILE GLY TYR HIS PRO GLU GLU LEU SEQRES 4 A 117 LEU GLY ARG SER ALA TYR GLU PHE TYR HIS ALA LEU ASP SEQRES 5 A 117 SER GLU ASN MET THR LYS SER HIS GLN ASN LEU CYS THR SEQRES 6 A 117 LYS GLY GLN VAL VAL SER GLY GLN TYR ARG MET LEU ALA SEQRES 7 A 117 LYS HIS GLY GLY TYR VAL TRP LEU GLU THR GLN GLY THR SEQRES 8 A 117 VAL ILE TYR ASN PRO ARG ASN LEU GLN PRO GLN CYS ILE SEQRES 9 A 117 MET CYS VAL ASN TYR VAL LEU SER GLU ILE GLU LYS ASN
HET 020 A 351 20
HETNAM 020 N-(FURAN-2-YLMETHYL)-2-NITRO-4-(TRIFLUOROMETHYL)ANILINE
FORMUL 3 020 C12 H9 F3 N2 O3 FORMUL 4 HOH *215(H2 O)
HELIX 1 1 ARG B 379 GLY B 385 1 7 HELIX 2 2 GLN B 387 LEU B 392 1 6 HELIX 3 3 ASN B 395 CYS B 400 5 6 HELIX 4 4 HIS B 401 GLU B 403 5 3 HELIX 5 5 ASP B 404 LEU B 418 1 15 HELIX 6 6 LEU A 239 SER A 241 5 3 HELIX 7 7 ARG A 260 GLY A 266 1 7 HELIX 8 8 HIS A 268 LEU A 273 1 6 HELIX 9 9 SER A 276 TYR A 281 5 6 HELIX 10 10 ASP A 285 GLY A 300 1 16
SHEET 1 A 5 PHE B 373 VAL B 376 0 SHEET 2 A 5 ARG B 362 HIS B 367 -1 N ARG B 366 O THR B 374 SHEET 3 A 5 TYR B 456 ASN B 463 -1 O CYS B 459 N SER B 365 SHEET 4 A 5 TRP B 436 PHE B 446 -1 N PHE B 444 O ILE B 458 SHEET 5 A 5 LEU B 423 ARG B 430 -1 N PHE B 427 O MET B 439 SHEET 1 B 5 PHE A 254 CYS A 257 0 SHEET 2 B 5 THR A 243 HIS A 248 -1 N GLU A 247 O THR A 255 SHEET 3 B 5 PRO A 334 VAL A 343 -1 O CYS A 339 N SER A 246 SHEET 4 B 5 TYR A 316 TYR A 327 -1 N ILE A 326 O GLN A 335 SHEET 5 B 5 GLN A 301 VAL A 303 -1 N VAL A 302 O GLY A 323 SHEET 1 C 5 PHE A 254 CYS A 257 0 SHEET 2 C 5 THR A 243 HIS A 248 -1 N GLU A 247 O THR A 255 SHEET 3 C 5 PRO A 334 VAL A 343 -1 O CYS A 339 N SER A 246 SHEET 4 C 5 TYR A 316 TYR A 327 -1 N ILE A 326 O GLN A 335 SHEET 5 C 5 TYR A 307 LEU A 310 -1 N TYR A 307 O LEU A 319
SITE 1 AC1 15 HIS A 248 MET A 252 PHE A 254 ALA A 277 SITE 2 AC1 15 TYR A 281 MET A 289 SER A 292 VAL A 302 SITE 3 AC1 15 SER A 304 TYR A 307 MET A 309 THR A 321 SITE 4 AC1 15 ILE A 337 CYS A 339 ASN A 341
CRYST1 40.889 70.280 42.348 90.00 108.68 90.00 P 1 21 1 2
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 0.024456 0.000000 0.008271 0.00000
SCALE2 0.000000 0.014229 0.000000 0.00000
SCALE3 0.000000 0.000000 0.024928 0.00000