HEADER DE NOVO PROTEIN 15-MAY-03 1PBZ TITLE DE NOVO DESIGNED PEPTIDE-METALLOPORPHYRIN COMPLEX, SOLUTION STRUCTURE CAVEAT 1PBZ INCORRECT CHIRALITY AT SOME CA COMPND MOL_ID: 1; COMPND 2 MOLECULE: DE NOVO DESIGNED CYCLIC PEPTIDE; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: COMPLEXED WITH METALLOPORPHYRIN SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: SYNTHESIZED BY SOLID STATE METHODS KEYWDS PEPTIDE; METALLOPORPHYRIN; HEME; DE NOVO DESIGN, DE NOVO PROTEIN EXPDTA SOLUTION NMR NUMMDL 14 AUTHOR J.WANG,M.M.ROSENBLATT,K.S.SUSLICK REVDAT 3 23-FEB-22 1PBZ 1 REMARK LINK REVDAT 2 24-FEB-09 1PBZ 1 VERSN REVDAT 1 09-DEC-03 1PBZ 0 JRNL AUTH M.M.ROSENBLATT,J.WANG,K.S.SUSLICK JRNL TITL DE NOVO DESIGNED CYCLIC-PEPTIDE HEME COMPLEXES JRNL REF PROC.NATL.ACAD.SCI.USA V. 100 13140 2003 JRNL REFN ISSN 0027-8424 JRNL PMID 14595023 JRNL DOI 10.1073/PNAS.2231273100 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : FELIX 98 REMARK 3 AUTHORS : ACCELRYS, INC REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1PBZ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-MAY-03. REMARK 100 THE DEPOSITION ID IS D_1000019221. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 277 REMARK 210 PH : 7.4 REMARK 210 IONIC STRENGTH : 50 MM POTASSIUM PHOSPHATE, 10 MM REMARK 210 POTASSIUM CHLORIDE REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 3MM CYCLIC PEPTIDE REMARK 210 METALLOPORPHYRIN COMPLEX REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : UNITY REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : NULL REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 40 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 14 REMARK 210 CONFORMERS, SELECTION CRITERIA : NO RESTRAINT VIOLATIONS GREATER REMARK 210 THAN 0.3 ANGSTROMS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: REMARK 210 IONIC_STRENGTH: 50MM PRESSURE: 1 ATM SOLVENT SYSTEM: AQUEOUS THE REMARK 210 STRUCTURE WAS DETERMINED USING 2D HOMONUCLEAR METHODS (WUTHRICH, REMARK 210 1986) REMARK 210 FOR RESONANCE ASSIGNMENTS GENERATION OF DISTANCE 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: 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 N NH2 A 18 O4 PC3 A 20 2.19 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 1 GLY B 16 CA - C - N ANGL. DEV. = -13.4 DEGREES REMARK 500 2 CYS A 17 N - CA - CB ANGL. DEV. = -12.7 DEGREES REMARK 500 2 ALA B 15 CB - CA - C ANGL. DEV. = 11.2 DEGREES REMARK 500 7 HIS B 9 CB - CA - C ANGL. DEV. = 12.4 DEGREES REMARK 500 8 CYS A 17 N - CA - CB ANGL. DEV. = -13.9 DEGREES REMARK 500 8 ALA B 15 N - CA - CB ANGL. DEV. = -8.4 DEGREES REMARK 500 9 HIS B 9 CB - CA - C ANGL. DEV. = 12.4 DEGREES REMARK 500 9 ALA B 13 N - CA - CB ANGL. DEV. = -8.6 DEGREES REMARK 500 10 HIS B 9 CB - CA - C ANGL. DEV. = 12.4 DEGREES REMARK 500 10 ALA B 10 N - CA - CB ANGL. DEV. = -9.0 DEGREES REMARK 500 11 CYS A 1 N - CA - CB ANGL. DEV. = -14.7 DEGREES REMARK 500 11 ALA A 13 N - CA - CB ANGL. DEV. = -9.0 DEGREES REMARK 500 11 CYS A 17 N - CA - CB ANGL. DEV. = -13.9 DEGREES REMARK 500 11 HIS B 9 CB - CA - C ANGL. DEV. = 13.2 DEGREES REMARK 500 11 ALA B 13 N - CA - CB ANGL. DEV. = -9.1 DEGREES REMARK 500 11 ALA B 15 N - CA - CB ANGL. DEV. = -13.3 DEGREES REMARK 500 13 GLY A 16 CA - C - N ANGL. DEV. = -14.2 DEGREES REMARK 500 13 CYS B 1 N - CA - CB ANGL. DEV. = -13.9 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 1 ALA A 12 -73.09 -63.29 REMARK 500 1 ALA A 13 -30.44 -31.94 REMARK 500 1 GLU A 14 -70.77 -74.21 REMARK 500 1 ALA B 12 -71.89 -56.35 REMARK 500 1 ALA B 13 -9.59 -45.72 REMARK 500 1 ALA B 15 56.07 -91.53 REMARK 500 2 ALA A 12 -79.42 -60.81 REMARK 500 2 ALA A 13 -39.07 -22.29 REMARK 500 2 GLU A 14 -70.40 -80.62 REMARK 500 2 ALA B 12 -70.07 -46.22 REMARK 500 2 ALA B 15 -122.13 -85.21 REMARK 500 3 ALA A 12 -78.11 -56.99 REMARK 500 3 ALA A 13 -24.84 -35.17 REMARK 500 3 GLU A 14 -71.26 -80.48 REMARK 500 3 ALA B 13 -30.81 -33.71 REMARK 500 3 GLU B 14 -92.46 -84.38 REMARK 500 4 ALA A 12 -78.11 -56.99 REMARK 500 4 ALA A 13 -24.84 -35.17 REMARK 500 4 GLU A 14 -71.26 -80.48 REMARK 500 4 ALA B 13 -30.81 -33.71 REMARK 500 4 GLU B 14 -92.46 -84.38 REMARK 500 5 ALA A 12 -70.05 -66.25 REMARK 500 5 ALA A 13 -30.09 -33.76 REMARK 500 5 GLU A 14 -75.43 -73.44 REMARK 500 5 ALA B 12 -75.27 -52.90 REMARK 500 5 ALA B 13 0.32 -49.30 REMARK 500 5 GLU B 14 -63.17 -97.07 REMARK 500 5 ALA B 15 56.19 -100.17 REMARK 500 6 ALA A 12 -75.07 -56.89 REMARK 500 6 ALA A 13 -41.21 -24.93 REMARK 500 6 ALA B 13 -34.99 -32.39 REMARK 500 6 GLU B 14 -73.65 -69.26 REMARK 500 7 ALA A 13 -31.54 -32.37 REMARK 500 7 ALA B 12 -73.54 -49.82 REMARK 500 7 ALA B 13 -26.71 -36.88 REMARK 500 7 GLU B 14 -77.67 -79.26 REMARK 500 8 ALA A 13 -30.63 -33.83 REMARK 500 8 GLU A 14 -74.21 -74.86 REMARK 500 8 ALA B 12 -77.07 -48.91 REMARK 500 8 ALA B 13 -6.60 -47.45 REMARK 500 8 GLU B 14 -63.86 -90.13 REMARK 500 8 ALA B 15 59.50 -101.05 REMARK 500 9 ALA A 12 -74.16 -63.15 REMARK 500 9 ALA A 13 -33.42 -27.65 REMARK 500 9 ALA B 12 -79.66 -53.46 REMARK 500 9 ALA B 13 -1.75 -46.96 REMARK 500 9 GLU B 14 -60.92 -100.17 REMARK 500 9 ALA B 15 56.67 -100.22 REMARK 500 10 ALA A 12 -74.02 -55.46 REMARK 500 10 ALA A 13 -14.25 -42.18 REMARK 500 REMARK 500 THIS ENTRY HAS 73 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 PC3 A 20 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 PC3 A 20 CO3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 9 NE2 REMARK 620 2 PC3 A 20 N2B 87.7 REMARK 620 3 PC3 A 20 N4B 87.7 91.0 REMARK 620 4 PC3 A 20 N6B 90.0 177.7 88.7 REMARK 620 5 PC3 A 20 N8B 93.4 90.9 177.9 89.5 REMARK 620 6 HIS B 9 NE2 177.1 92.5 89.4 89.8 89.5 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PC3 A 20 DBREF 1PBZ A 0 18 PDB 1PBZ 1PBZ 0 18 DBREF 1PBZ B 0 18 PDB 1PBZ 1PBZ 0 18 SEQRES 1 A 19 ACE CYS GLY ALA GLU ALA ALA LYS ALA HIS ALA LYS ALA SEQRES 2 A 19 ALA GLU ALA GLY CYS NH2 SEQRES 1 B 19 ACE CYS GLY ALA GLU ALA ALA LYS ALA HIS ALA LYS ALA SEQRES 2 B 19 ALA GLU ALA GLY CYS NH2 HET ACE A 0 6 HET NH2 A 18 3 HET ACE B 0 6 HET NH2 B 18 3 HET PC3 A 20 81 HETNAM ACE ACETYL GROUP HETNAM NH2 AMINO GROUP HETNAM PC3 COPROPORPHYRIN I CONTAINING CO(III) FORMUL 1 ACE 2(C2 H4 O) FORMUL 1 NH2 2(H2 N) FORMUL 3 PC3 C36 H36 CO N4 O8 HELIX 1 1 GLY A 2 GLY A 16 1 15 HELIX 2 2 GLY B 2 ALA B 15 1 14 SSBOND 1 CYS A 1 CYS B 1 1555 1555 2.00 SSBOND 2 CYS A 17 CYS B 17 1555 1555 2.01 LINK C ACE A 0 N CYS A 1 1555 1555 1.33 LINK C CYS A 17 N NH2 A 18 1555 1555 1.32 LINK C ACE B 0 N CYS B 1 1555 1555 1.33 LINK C CYS B 17 N NH2 B 18 1555 1555 1.32 LINK NE2 HIS A 9 CO3 PC3 A 20 1555 1555 2.24 LINK CO3 PC3 A 20 NE2 HIS B 9 1555 1555 2.27 SITE 1 AC1 10 CYS A 1 ALA A 5 HIS A 9 ALA A 12 SITE 2 AC1 10 CYS A 17 NH2 A 18 CYS B 1 ALA B 8 SITE 3 AC1 10 HIS B 9 CYS B 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 MODEL 1 HETATM 1 C ACE A 0 -5.752 -5.859 1.738 1.00 0.00 C HETATM 2 O ACE A 0 -6.396 -6.009 2.769 1.00 0.00 O HETATM 3 CH3 ACE A 0 -4.936 -7.026 1.194 1.00 0.00 C HETATM 4 H1 ACE A 0 -3.876 -6.743 1.069 1.00 0.00 H HETATM 5 H2 ACE A 0 -5.332 -7.360 0.220 1.00 0.00 H HETATM 6 H3 ACE A 0 -4.976 -7.882 1.889 1.00 0.00 H