HEADER CYTOKINE 17-DEC-98 1ILQ TITLE CXCR-1 N-TERMINAL PEPTIDE BOUND TO INTERLEUKIN-8 (MINIMIZED MEAN) COMPND MOL_ID: 1; COMPND 2 MOLECULE: INTERLEUKIN-8 PRECURSOR; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: IL-8; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: INTERLEUKIN-8 RECEPTOR A; COMPND 8 CHAIN: C; COMPND 9 FRAGMENT: 9-29; COMPND 10 SYNONYM: IL8-RA; COMPND 11 ENGINEERED: YES; COMPND 12 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI K12; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 83333; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: K12; SOURCE 8 EXPRESSION_SYSTEM_CELLULAR_LOCATION: PERIPLASM; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: ALKALINE PHOSPHATASE PROMOTER (PPHOA); SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PPS0170; SOURCE 12 MOL_ID: 2; SOURCE 13 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 14 ORGANISM_COMMON: HUMAN; SOURCE 15 ORGANISM_TAXID: 9606 KEYWDS CYTOKINE EXPDTA SOLUTION NMR AUTHOR N.J.SKELTON,C.QUAN,H.LOWMAN REVDAT 6 23-OCT-24 1ILQ 1 REMARK REVDAT 5 15-NOV-23 1ILQ 1 LINK ATOM REVDAT 4 23-FEB-22 1ILQ 1 REMARK LINK REVDAT 3 24-FEB-09 1ILQ 1 VERSN REVDAT 2 22-DEC-99 1ILQ 4 HEADER COMPND REMARK JRNL REVDAT 2 2 4 ATOM SOURCE SEQRES REVDAT 1 23-DEC-98 1ILQ 0 JRNL AUTH N.J.SKELTON,C.QUAN,D.REILLY,H.LOWMAN JRNL TITL STRUCTURE OF A CXC CHEMOKINE-RECEPTOR FRAGMENT IN COMPLEX JRNL TITL 2 WITH INTERLEUKIN-8. JRNL REF STRUCTURE FOLD.DES. V. 7 157 1999 JRNL REFN ISSN 0969-2126 JRNL PMID 10368283 JRNL DOI 10.1016/S0969-2126(99)80022-7 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.R.ATTWOOD,ET AL. REMARK 1 TITL PEPTIDE BASED INHIBITORS OF IL-8: STRUCTURAL SIMPLIFICATION REMARK 1 TITL 2 AND IMPROVED POTENCY REMARK 1 REF BIOORG.MED.CHEM.LETT. V. 7 429 1997 REMARK 1 REFN ISSN 0960-894X REMARK 1 REFERENCE 2 REMARK 1 AUTH G.M.CLORE,E.APPELLA,M.YAMADA,A.M.GRONENBORN REMARK 1 TITL THREE-DIMENSIONAL STRUCTURE OF IL-8 IN SOLUTION REMARK 1 REF BIOCHEMISTRY V. 29 1689 1990 REMARK 1 REFN ISSN 0006-2960 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : BIOSYM REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: INITIAL COORDINATES FOR IL-8 WERE TAKEN REMARK 3 FROM PDB ENTRY 1IL8; A LINEAR CHAIN FOR THE CXCR-1 FRAGMENT WAS REMARK 3 BUILT IN INSIGHT (MSI). THE CXCR-1 FRAGMENT WAS POSITIONED REMARK 3 RANDOMLY WITH RESPECT TO IL8 - OBTAIN 40 STARTING CONFORMATIONS. REMARK 3 THE INITIAL STRUCTURES WERE THEN REFINED USING RMD WITH THE REMARK 3 AMBER ALL ATOM FORCE FIELD AS IMPLIMENTED WITHIN DISCOVER. ALL REMARK 3 OF IL8 MONOMER B AND PARTS OF IL8 MONOMER A (2-7, 22-38 AND 51- REMARK 3 72) WERE KEPT FIXED DURING THE REFINEMENT SINCE CHEMICAL SHIFT REMARK 3 CHANGES INDICATED THAT THESE PORTION OF THE MOLECULE WERE NOT REMARK 3 PERTURBED BY PEPTIDE BINDING. THIS MODEL IS THE RESULT OF REMARK 3 RESTRAINED ENERGY MINIMIZATION OF THE GEOMETRIC MEAN OF 20 REMARK 3 STRUCTURES FROM THE ENSEMBLE (ENTRY 1ILP) SEE JRNL ENTRY FOR REMARK 3 MORE DETAILS. REMARK 4 REMARK 4 1ILQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000174185. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 308.00 REMARK 210 PH : 5.50 REMARK 210 IONIC STRENGTH : 0.15 M REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : ASSIGNMENT: SEE REFERENCE 1; REMARK 210 RESTRAINTS: 3D 15N-EDITED-NOESY REMARK 210 HSQC; 3D 13C-FILTERED; 13C- REMARK 210 EDITED-NOESY HMQC; 2D 15N- REMARK 210 FILTERED NOESY; 2D 13C-FILTERED REMARK 210 NOESY (100MS); 15N-FILTERED REMARK 210 NOESY (ALL MIXING TIMES = 100 MS) REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : AMX 500 REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : MSI DISCOVER DISCOVER DISCOVER REMARK 210 METHOD USED : RESTRAINED MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 40 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : LEAST RESTRAINT VIOLATION ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: THE ASSIGNMENTS WERE MADE USING TRIPLE RESONANCE NMR REMARK 210 EXPERIMENTS CONDUCTED ON 13C/15N LABELED IL-8 BOUND TO UNLABELED REMARK 210 CXCR-1 PEPTIDE (SEE JRNL ENTRY FOR MORE DETAILS) NOE RESTRAINTS REMARK 210 WERE OBTAINED FROM 15N EDITED EXPERIMENTS (INTRA IL8), 13C OR REMARK 210 15N FILTERED EXPERIMENTS (INTRA CXCR-1) OR 13C-FILTERED/ EDITED REMARK 210 EXPERIMENTS (INTERMOLECULAR RESTRAINTS) REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 RES C SSSEQI REMARK 465 SER A 1 REMARK 465 SER B 1 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 TRP A 57 CG TRP A 57 CD2 -0.108 REMARK 500 HIS B 18 NE2 HIS B 18 CD2 -0.076 REMARK 500 TRP B 57 CG TRP B 57 CD2 -0.110 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 TRP A 57 CG - CD1 - NE1 ANGL. DEV. = -6.3 DEGREES REMARK 500 TRP A 57 CD1 - NE1 - CE2 ANGL. DEV. = 5.5 DEGREES REMARK 500 TRP A 57 NE1 - CE2 - CZ2 ANGL. DEV. = 8.9 DEGREES REMARK 500 TRP A 57 NE1 - CE2 - CD2 ANGL. DEV. = -6.9 DEGREES REMARK 500 TRP B 57 CG - CD1 - NE1 ANGL. DEV. = -6.4 DEGREES REMARK 500 TRP B 57 CD1 - NE1 - CE2 ANGL. DEV. = 5.6 DEGREES REMARK 500 TRP B 57 NE1 - CE2 - CZ2 ANGL. DEV. = 9.0 DEGREES REMARK 500 TRP B 57 NE1 - CE2 - CD2 ANGL. DEV. = -7.0 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 LYS A 3 -66.54 -130.81 REMARK 500 ASN A 36 -149.51 -140.28 REMARK 500 PRO A 53 -2.56 -59.24 REMARK 500 LYS B 3 -66.57 -130.86 REMARK 500 SER B 14 37.75 -99.02 REMARK 500 ASN B 36 -149.44 -140.28 REMARK 500 ASP B 45 -6.26 -59.16 REMARK 500 PRO B 53 -2.55 -59.37 REMARK 500 PHE C 4 -174.95 -65.89 REMARK 500 PRO C 9 -179.30 -56.77 REMARK 500 GLU C 13 102.64 -162.36 REMARK 500 ASP C 14 47.40 -146.37 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 6 0.32 SIDE CHAIN REMARK 500 ARG A 26 0.22 SIDE CHAIN REMARK 500 ARG A 60 0.21 SIDE CHAIN REMARK 500 ARG B 6 0.32 SIDE CHAIN REMARK 500 ARG B 26 0.22 SIDE CHAIN REMARK 500 ARG B 47 0.31 SIDE CHAIN REMARK 500 ARG B 60 0.21 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NH2 C 18 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1ILP RELATED DB: PDB DBREF 1ILQ A 1 72 UNP P10145 IL8_HUMAN 28 99 DBREF 1ILQ B 1 72 UNP P10145 IL8_HUMAN 28 99 DBREF 1ILQ C 1 17 UNP P25024 CXCR1_HUMAN 20 29 SEQADV 1ILQ ACA C 7 UNP P25024 LEU 15 SEE REMARK 999 SEQADV 1ILQ C UNP P25024 ASN 16 SEE REMARK 999 SEQADV 1ILQ C UNP P25024 PHE 17 SEE REMARK 999 SEQADV 1ILQ C UNP P25024 THR 18 SEE REMARK 999 SEQADV 1ILQ C UNP P25024 GLY 19 SEE REMARK 999 SEQRES 1 A 72 SER ALA LYS GLU LEU ARG CYS GLN CYS ILE LYS THR TYR SEQRES 2 A 72 SER LYS PRO PHE HIS PRO LYS PHE ILE LYS GLU LEU ARG SEQRES 3 A 72 VAL ILE GLU SER GLY PRO HIS CYS ALA ASN THR GLU ILE SEQRES 4 A 72 ILE VAL LYS LEU SER ASP GLY ARG GLU LEU CYS LEU ASP SEQRES 5 A 72 PRO LYS GLU ASN TRP VAL GLN ARG VAL VAL GLU LYS PHE SEQRES 6 A 72 LEU LYS ARG ALA GLU ASN SER SEQRES 1 B 72 SER ALA LYS GLU LEU ARG CYS GLN CYS ILE LYS THR TYR SEQRES 2 B 72 SER LYS PRO PHE HIS PRO LYS PHE ILE LYS GLU LEU ARG SEQRES 3 B 72 VAL ILE GLU SER GLY PRO HIS CYS ALA ASN THR GLU ILE SEQRES 4 B 72 ILE VAL LYS LEU SER ASP GLY ARG GLU LEU CYS LEU ASP SEQRES 5 B 72 PRO LYS GLU ASN TRP VAL GLN ARG VAL VAL GLU LYS PHE SEQRES 6 B 72 LEU LYS ARG ALA GLU ASN SER SEQRES 1 C 19 ACE MET TRP ASP PHE ASP ASP ACA MET PRO PRO ALA ASP SEQRES 2 C 19 GLU ASP TYR SER PRO NH2 HET ACE C 0 6 HET ACA C 7 19 HET NH2 C 18 3 HETNAM ACE ACETYL GROUP HETNAM ACA 6-AMINOHEXANOIC ACID HETNAM NH2 AMINO GROUP HETSYN ACA AMINOCAPROIC ACID FORMUL 3 ACE C2 H4 O FORMUL 3 ACA C6 H13 N O2 FORMUL 3 NH2 H2 N HELIX 1 1 PRO A 19 PHE A 21 5 3 HELIX 2 2 ASN A 56 GLU A 70 1 15 HELIX 3 3 PRO B 19 PHE B 21 5 3 HELIX 4 4 ASN B 56 GLU B 70 1 15 SHEET 1 A 3 GLU A 48 LEU A 51 0 SHEET 2 A 3 GLU A 38 LEU A 43 -1 N VAL A 41 O LEU A 49 SHEET 3 A 3 ILE A 22 ILE A 28 -1 N ILE A 28 O GLU A 38 SHEET 1 B 3 ARG B 47 LEU B 51 0 SHEET 2 B 3 GLU B 38 LEU B 43 -1 N LEU B 43 O ARG B 47 SHEET 3 B 3 ILE B 22 ILE B 28 -1 N ILE B 28 O GLU B 38 SSBOND 1 CYS A 7 CYS A 34 1555 1555 2.02 SSBOND 2 CYS A 9 CYS A 50 1555 1555 2.04 SSBOND 3 CYS B 7 CYS B 34 1555 1555 2.02 SSBOND 4 CYS B 9 CYS B 50 1555 1555 2.02 LINK C ACE C 0 N MET C 1 1555 1555 1.34 LINK C ASP C 6 N ACA C 7 1555 1555 1.34 LINK C ACA C 7 N MET C 8 1555 1555 1.34 LINK C PRO C 17 N NH2 C 18 1555 1555 1.33 SITE 1 AC2 2 GLN A 8 PRO C 17 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000