HEADER TRANSCRIPTION 09-DEC-17 5YYF TITLE CRYSTAL STRUCTURE OF AF9 YEATS DOMAIN IN COMPLEX WITH A PEPTIDE TITLE 2 INHIBITOR "PHQ-H3(Q5-K9)" MODIFIED AT K9 WITH 2-FURANCARBOYL GROUP COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN AF-9; COMPND 3 CHAIN: A, C; COMPND 4 SYNONYM: ALL1-FUSED GENE FROM CHROMOSOME 9 PROTEIN,MYELOID/LYMPHOID COMPND 5 OR MIXED-LINEAGE LEUKEMIA TRANSLOCATED TO CHROMOSOME 3 PROTEIN,YEATS COMPND 6 DOMAIN-CONTAINING PROTEIN 3; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: PEPTIDE INHIBITOR PHQ-H3(Q5-K9); COMPND 10 CHAIN: B, D; COMPND 11 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: MLLT3, AF9, YEATS3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-28B; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_TAXID: 9606 KEYWDS YEATS DOMAIN, COMPLEX, INHIBITOR, 2-FURANCARBOYL GROUP, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR Y.LI,H.LI REVDAT 4 22-NOV-23 5YYF 1 REMARK REVDAT 3 16-SEP-20 5YYF 1 TITLE REVDAT 2 28-NOV-18 5YYF 1 JRNL REVDAT 1 07-NOV-18 5YYF 0 JRNL AUTH X.LI,X.M.LI,Y.JIANG,Z.LIU,Y.CUI,K.Y.FUNG, JRNL AUTH 2 S.H.E.VAN DER BEELEN,G.TIAN,L.WAN,X.SHI,C.D.ALLIS,H.LI,Y.LI, JRNL AUTH 3 X.D.LI JRNL TITL STRUCTURE-GUIDED DEVELOPMENT OF YEATS DOMAIN INHIBITORS BY JRNL TITL 2 TARGETING PI-PI-PI STACKING. JRNL REF NAT. CHEM. BIOL. V. 14 1140 2018 JRNL REFN ESSN 1552-4469 JRNL PMID 30374167 JRNL DOI 10.1038/S41589-018-0144-Y REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.12RC1_2801: ???) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.29 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 27771 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 1398 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 42.2964 - 4.0991 0.99 2714 171 0.1702 0.1604 REMARK 3 2 4.0991 - 3.2540 0.99 2641 159 0.1734 0.1908 REMARK 3 3 3.2540 - 2.8427 1.00 2673 121 0.2014 0.2357 REMARK 3 4 2.8427 - 2.5829 1.00 2648 130 0.2295 0.2855 REMARK 3 5 2.5829 - 2.3977 1.00 2663 136 0.2345 0.3452 REMARK 3 6 2.3977 - 2.2564 1.00 2669 132 0.2382 0.2958 REMARK 3 7 2.2564 - 2.1434 1.00 2616 154 0.2339 0.2687 REMARK 3 8 2.1434 - 2.0501 1.00 2594 134 0.2374 0.2596 REMARK 3 9 2.0501 - 1.9712 1.00 2665 128 0.2492 0.2788 REMARK 3 10 1.9712 - 1.9032 0.95 2490 133 0.2740 0.3065 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.740 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 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 : 0.008 2513 REMARK 3 ANGLE : 0.861 3379 REMARK 3 CHIRALITY : 0.048 339 REMARK 3 PLANARITY : 0.004 439 REMARK 3 DIHEDRAL : 15.414 1495 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 5YYF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 11-JAN-18. REMARK 100 THE DEPOSITION ID IS D_1300006122. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-OCT-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27771 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 42.286 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 5.100 REMARK 200 R MERGE (I) : 0.10200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 25.7800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.89700 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: MOLREP REMARK 200 STARTING MODEL: 4TMP REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.57 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M AMMONIUM SULFATE, 0.1M SODIUM REMARK 280 CITRATE TRIBASIC DIHYDRATE, PH 5.6, 25 % (W/V) PEG 4000, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 45.76800 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.99600 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 45.76800 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 21.99600 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 413 LIES ON A SPECIAL POSITION. REMARK 400 REMARK 400 COMPOUND REMARK 400 REMARK 400 THE PHQ-H3(Q5-K9) PEPTIDE MODIFIED AT K9 WITH 2-FURANCARBOYL GROUP REMARK 400 IS PEPTIDE-LIKE, A MEMBER OF INHIBITOR CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: PHQ-H3(Q5-K9) PEPTIDE MODIFIED AT K9 WITH 2-FURANCARBOYL REMARK 400 GROUP REMARK 400 CHAIN: B, D REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER REMARK 400 COMPONENT_2: RESIDUE FOA REMARK 400 DESCRIPTION: NULL 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 A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 GLY C -2 REMARK 465 SER C -1 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 HIS C 0 CG ND1 CD2 CE1 NE2 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 HOH C 374 O HOH C 382 1.74 REMARK 500 O HOH A 356 O HOH A 434 1.83 REMARK 500 O HOH C 367 O HOH C 387 1.89 REMARK 500 O HOH A 429 O HOH A 434 1.92 REMARK 500 O HOH A 315 O HOH A 355 1.96 REMARK 500 N VAL C 19 O HOH C 301 1.97 REMARK 500 NH2 ARG A 16 O HOH A 301 2.01 REMARK 500 O HOH A 372 O HOH A 430 2.03 REMARK 500 O LYS C 21 O HOH C 302 2.04 REMARK 500 O THR C 29 O HOH C 303 2.08 REMARK 500 O HOH A 439 O HOH C 322 2.10 REMARK 500 O HOH A 420 O HOH A 439 2.15 REMARK 500 O HOH C 342 O HOH C 364 2.18 REMARK 500 NE ARG A 16 O HOH A 302 2.19 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 O HOH C 377 O HOH C 395 2555 1.66 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 PRO A 70 C - N - CD ANGL. DEV. = 18.1 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 GLU A 93 -167.90 -103.20 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 SO4 A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FOA B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 C 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide PHQ D 4 and GLN D 5 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide LYS D 9 and NH2 D 10 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide FOA D 101 and LYS D REMARK 800 9 DBREF 5YYF A 1 138 UNP P42568 AF9_HUMAN 1 138 DBREF 5YYF B 4 10 PDB 5YYF 5YYF 4 10 DBREF 5YYF C 1 138 UNP P42568 AF9_HUMAN 1 138 DBREF 5YYF D 4 10 PDB 5YYF 5YYF 4 10 SEQADV 5YYF GLY A -2 UNP P42568 EXPRESSION TAG SEQADV 5YYF SER A -1 UNP P42568 EXPRESSION TAG SEQADV 5YYF HIS A 0 UNP P42568 EXPRESSION TAG SEQADV 5YYF GLY C -2 UNP P42568 EXPRESSION TAG SEQADV 5YYF SER C -1 UNP P42568 EXPRESSION TAG SEQADV 5YYF HIS C 0 UNP P42568 EXPRESSION TAG SEQRES 1 A 141 GLY SER HIS MET ALA SER SER CYS ALA VAL GLN VAL LYS SEQRES 2 A 141 LEU GLU LEU GLY HIS ARG ALA GLN VAL ARG LYS LYS PRO SEQRES 3 A 141 THR VAL GLU GLY PHE THR HIS ASP TRP MET VAL PHE VAL SEQRES 4 A 141 ARG GLY PRO GLU HIS SER ASN ILE GLN HIS PHE VAL GLU SEQRES 5 A 141 LYS VAL VAL PHE HIS LEU HIS GLU SER PHE PRO ARG PRO SEQRES 6 A 141 LYS ARG VAL CYS LYS ASP PRO PRO TYR LYS VAL GLU GLU SEQRES 7 A 141 SER GLY TYR ALA GLY PHE ILE LEU PRO ILE GLU VAL TYR SEQRES 8 A 141 PHE LYS ASN LYS GLU GLU PRO ARG LYS VAL ARG PHE ASP SEQRES 9 A 141 TYR ASP LEU PHE LEU HIS LEU GLU GLY HIS PRO PRO VAL SEQRES 10 A 141 ASN HIS LEU ARG CYS GLU LYS LEU THR PHE ASN ASN PRO SEQRES 11 A 141 THR GLU ASP PHE ARG ARG LYS LEU LEU LYS ALA SEQRES 1 B 7 PHQ GLN THR ALA ARG LYS NH2 SEQRES 1 C 141 GLY SER HIS MET ALA SER SER CYS ALA VAL GLN VAL LYS SEQRES 2 C 141 LEU GLU LEU GLY HIS ARG ALA GLN VAL ARG LYS LYS PRO SEQRES 3 C 141 THR VAL GLU GLY PHE THR HIS ASP TRP MET VAL PHE VAL SEQRES 4 C 141 ARG GLY PRO GLU HIS SER ASN ILE GLN HIS PHE VAL GLU SEQRES 5 C 141 LYS VAL VAL PHE HIS LEU HIS GLU SER PHE PRO ARG PRO SEQRES 6 C 141 LYS ARG VAL CYS LYS ASP PRO PRO TYR LYS VAL GLU GLU SEQRES 7 C 141 SER GLY TYR ALA GLY PHE ILE LEU PRO ILE GLU VAL TYR SEQRES 8 C 141 PHE LYS ASN LYS GLU GLU PRO ARG LYS VAL ARG PHE ASP SEQRES 9 C 141 TYR ASP LEU PHE LEU HIS LEU GLU GLY HIS PRO PRO VAL SEQRES 10 C 141 ASN HIS LEU ARG CYS GLU LYS LEU THR PHE ASN ASN PRO SEQRES 11 C 141 THR GLU ASP PHE ARG ARG LYS LEU LEU LYS ALA SEQRES 1 D 7 PHQ GLN THR ALA ARG LYS NH2 HET PHQ B 4 10 HET NH2 B 10 1 HET PHQ D 4 10 HET NH2 D 10 1 HET SO4 A 201 5 HET SO4 A 202 5 HET FOA B 101 7 HET SO4 C 201 5 HET FOA D 101 7 HETNAM PHQ BENZYL CHLOROCARBONATE HETNAM NH2 AMINO GROUP HETNAM SO4 SULFATE ION HETNAM FOA 2-FUROIC ACID FORMUL 2 PHQ 2(C8 H7 CL O2) FORMUL 2 NH2 2(H2 N) FORMUL 5 SO4 3(O4 S 2-) FORMUL 7 FOA 2(C5 H4 O3) FORMUL 10 HOH *278(H2 O) HELIX 1 AA1 GLY A 38 SER A 42 5 5 HELIX 2 AA2 THR A 128 LEU A 136 1 9 HELIX 3 AA3 GLY C 38 SER C 42 5 5 HELIX 4 AA4 THR C 128 ALA C 138 1 11 SHEET 1 AA1 4 TYR A 71 GLY A 77 0 SHEET 2 AA1 4 HIS A 30 ARG A 37 -1 N TRP A 32 O GLU A 75 SHEET 3 AA1 4 ALA A 6 VAL A 19 -1 N GLU A 12 O ARG A 37 SHEET 4 AA1 4 VAL A 114 ASN A 125 -1 O ARG A 118 N LEU A 13 SHEET 1 AA2 4 LYS A 63 CYS A 66 0 SHEET 2 AA2 4 VAL A 48 HIS A 54 -1 N PHE A 53 O ARG A 64 SHEET 3 AA2 4 PHE A 81 PHE A 89 -1 O GLU A 86 N VAL A 52 SHEET 4 AA2 4 LYS A 97 LEU A 104 -1 O TYR A 102 N LEU A 83 SHEET 1 AA3 4 TYR C 71 GLY C 77 0 SHEET 2 AA3 4 HIS C 30 ARG C 37 -1 N HIS C 30 O GLY C 77 SHEET 3 AA3 4 ALA C 6 VAL C 19 -1 N GLU C 12 O ARG C 37 SHEET 4 AA3 4 VAL C 114 ASN C 125 -1 O ARG C 118 N LEU C 13 SHEET 1 AA4 4 LYS C 63 CYS C 66 0 SHEET 2 AA4 4 VAL C 48 HIS C 54 -1 N PHE C 53 O ARG C 64 SHEET 3 AA4 4 PHE C 81 PHE C 89 -1 O GLU C 86 N VAL C 52 SHEET 4 AA4 4 LYS C 97 LEU C 104 -1 O TYR C 102 N LEU C 83 LINK C1 PHQ B 4 N GLN B 5 1555 1555 1.43 LINK C LYS B 9 N NH2 B 10 1555 1555 1.39 LINK NZ LYS B 9 C1 FOA B 101 1555 1555 1.40 LINK C1 PHQ D 4 N GLN D 5 1555 1555 1.30 LINK C LYS D 9 N NH2 D 10 1555 1555 1.39 LINK NZ LYS D 9 C1 FOA D 101 1555 1555 1.40 CISPEP 1 PRO A 69 PRO A 70 0 -0.78 CISPEP 2 GLU A 94 PRO A 95 0 -1.70 CISPEP 3 PRO C 69 PRO C 70 0 -0.37 CISPEP 4 GLU C 94 PRO C 95 0 -2.91 SITE 1 AC1 7 ARG A 16 MET A 33 PHE A 35 ARG A 37 SITE 2 AC1 7 HOH A 356 HOH A 366 HOH A 389 SITE 1 AC2 3 HIS A 54 PRO A 84 ARG A 99 SITE 1 AC3 9 PHE A 28 SER A 58 PHE A 59 SER A 76 SITE 2 AC3 9 GLY A 77 TYR A 78 ALA A 79 HOH A 334 SITE 3 AC3 9 LYS B 9 SITE 1 AC4 2 PHE C 35 ARG C 37 SITE 1 AC5 9 ARG A 99 PHE C 105 LEU C 106 HIS C 107 SITE 2 AC5 9 LEU C 108 HIS C 111 HOH C 330 THR D 6 SITE 3 AC5 9 ARG D 8 SITE 1 AC6 9 HIS C 56 SER C 58 PHE C 59 GLY C 80 SITE 2 AC6 9 PHE C 81 ARG D 8 FOA D 101 HOH D 202 SITE 3 AC6 9 HOH D 206 SITE 1 AC7 13 PHE C 28 SER C 58 PHE C 59 SER C 76 SITE 2 AC7 13 GLY C 77 TYR C 78 ALA C 79 GLY C 80 SITE 3 AC7 13 PHE C 81 ARG D 8 NH2 D 10 HOH D 202 SITE 4 AC7 13 HOH D 204 CRYST1 91.536 43.992 89.053 90.00 95.86 90.00 C 1 2 1 8 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 0.010925 0.000000 0.001120 0.00000 SCALE2 0.000000 0.022731 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011288 0.00000