HEADER DE NOVO PROTEIN 13-FEB-17 5US3 TITLE HETEROGENEOUS-BACKBONE FOLDAMER MIMIC OF THE SP1-3 ZINC FINGER COMPND MOL_ID: 1; COMPND 2 MOLECULE: HETEROGENEOUS-BACKBONE VARIANT OF THE SP1-3 ZINC FINGER: N- COMPND 3 ME-ALA3, N-ME-ARG10, BETA-3-ASP15, BETA-3-LYS19, BETA3-LYS22, BETA-3- COMPND 4 GLN25; COMPND 5 CHAIN: A; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_TAXID: 9606 KEYWDS ZINC FINGER, HETEROGENEOUS BACKBONE, FOLDAMER, DE NOVO PROTEIN EXPDTA SOLUTION NMR NUMMDL 9 AUTHOR K.L.GEORGE,W.S.HORNE REVDAT 6 15-NOV-23 5US3 1 ATOM REVDAT 5 14-JUN-23 5US3 1 REMARK REVDAT 4 01-JAN-20 5US3 1 REMARK REVDAT 3 13-SEP-17 5US3 1 REMARK REVDAT 2 21-JUN-17 5US3 1 JRNL REVDAT 1 31-MAY-17 5US3 0 JRNL AUTH K.L.GEORGE,W.S.HORNE JRNL TITL HETEROGENEOUS-BACKBONE FOLDAMER MIMICS OF ZINC FINGER JRNL TITL 2 TERTIARY STRUCTURE. JRNL REF J. AM. CHEM. SOC. V. 139 7931 2017 JRNL REFN ESSN 1520-5126 JRNL PMID 28509549 JRNL DOI 10.1021/JACS.7B03114 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.3 REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5US3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-FEB-17. REMARK 100 THE DEPOSITION ID IS D_1000226411. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 277 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 5 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.2 MM NA DSS, 1.5 MM NA ZINC REMARK 210 CHLORIDE, 1.25 MM NA PEPTIDE, 9: REMARK 210 1 H2O/D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D TOCSY; 2D COSY; 2D NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, SPARKY, CNS 1.3 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 9 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 100 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 2970 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 O CYS A 7 H LYS A 9 1.45 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 B3K A 22 CA - C - N ANGL. DEV. = -19.9 DEGREES REMARK 500 1 B3Q A 25 CA - C - N ANGL. DEV. = 27.3 DEGREES REMARK 500 2 B3K A 22 CA - C - N ANGL. DEV. = -19.8 DEGREES REMARK 500 2 B3Q A 25 CA - C - N ANGL. DEV. = 25.8 DEGREES REMARK 500 3 B3K A 22 CA - C - N ANGL. DEV. = -19.5 DEGREES REMARK 500 3 B3Q A 25 CA - C - N ANGL. DEV. = 28.5 DEGREES REMARK 500 4 B3K A 22 CA - C - N ANGL. DEV. = -19.8 DEGREES REMARK 500 4 B3Q A 25 CA - C - N ANGL. DEV. = 27.4 DEGREES REMARK 500 5 B3K A 22 CA - C - N ANGL. DEV. = -19.8 DEGREES REMARK 500 5 B3Q A 25 CA - C - N ANGL. DEV. = 25.9 DEGREES REMARK 500 6 B3K A 22 CA - C - N ANGL. DEV. = -19.7 DEGREES REMARK 500 6 B3Q A 25 CA - C - N ANGL. DEV. = 26.6 DEGREES REMARK 500 7 B3K A 22 CA - C - N ANGL. DEV. = -19.8 DEGREES REMARK 500 7 B3Q A 25 CA - C - N ANGL. DEV. = 27.3 DEGREES REMARK 500 8 B3K A 22 CA - C - N ANGL. DEV. = -19.3 DEGREES REMARK 500 8 B3Q A 25 CA - C - N ANGL. DEV. = 26.6 DEGREES REMARK 500 9 B3K A 22 CA - C - N ANGL. DEV. = -18.6 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 MAA A 3 153.30 68.94 REMARK 500 1 PRO A 8 25.90 -45.12 REMARK 500 1 PHE A 11 -100.10 -109.47 REMARK 500 1 NLE A 12 -6.21 -177.40 REMARK 500 2 TYR A 2 144.30 64.36 REMARK 500 2 MAA A 3 156.51 66.89 REMARK 500 2 PRO A 8 43.88 -54.19 REMARK 500 2 MMO A 10 126.71 28.00 REMARK 500 2 PHE A 11 -84.74 -128.89 REMARK 500 2 NLE A 12 -6.60 -177.87 REMARK 500 3 MAA A 3 159.96 69.16 REMARK 500 3 PRO A 8 44.02 -55.24 REMARK 500 3 MMO A 10 127.03 20.60 REMARK 500 3 PHE A 11 -83.37 -127.19 REMARK 500 3 NLE A 12 -6.21 -178.85 REMARK 500 4 MAA A 3 161.78 71.03 REMARK 500 4 PRO A 8 45.45 -55.01 REMARK 500 4 MMO A 10 126.97 23.23 REMARK 500 4 PHE A 11 -79.40 -127.52 REMARK 500 4 NLE A 12 -15.89 -173.10 REMARK 500 5 MAA A 3 159.52 68.18 REMARK 500 5 PRO A 8 47.07 -56.86 REMARK 500 5 MMO A 10 123.79 39.58 REMARK 500 5 ASN A 26 122.86 64.60 REMARK 500 6 MAA A 3 157.46 67.53 REMARK 500 6 PRO A 8 46.20 -53.80 REMARK 500 6 MMO A 10 125.01 33.00 REMARK 500 7 MAA A 3 163.53 73.71 REMARK 500 7 PRO A 8 46.31 -55.89 REMARK 500 7 MMO A 10 126.04 30.90 REMARK 500 7 PHE A 11 -78.02 -127.68 REMARK 500 7 NLE A 12 -12.36 -172.95 REMARK 500 8 MAA A 3 163.22 71.45 REMARK 500 8 PRO A 8 32.96 -38.74 REMARK 500 8 NLE A 12 48.15 -74.43 REMARK 500 8 ASN A 26 131.30 63.66 REMARK 500 9 MAA A 3 153.52 68.51 REMARK 500 9 PRO A 8 43.67 -53.98 REMARK 500 9 MMO A 10 127.45 24.24 REMARK 500 9 PHE A 11 -86.78 -128.61 REMARK 500 9 NLE A 12 -2.46 179.23 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 B3D A 15 HIS A 16 1 142.77 REMARK 500 B3K A 19 HIS A 20 1 146.19 REMARK 500 B3D A 15 HIS A 16 2 141.87 REMARK 500 B3K A 19 HIS A 20 2 146.05 REMARK 500 B3D A 15 HIS A 16 3 142.11 REMARK 500 B3K A 19 HIS A 20 3 146.14 REMARK 500 B3D A 15 HIS A 16 4 140.99 REMARK 500 B3K A 19 HIS A 20 4 145.96 REMARK 500 B3D A 15 HIS A 16 5 141.34 REMARK 500 B3K A 19 HIS A 20 5 146.31 REMARK 500 B3D A 15 HIS A 16 6 141.29 REMARK 500 B3K A 19 HIS A 20 6 146.22 REMARK 500 B3D A 15 HIS A 16 7 141.85 REMARK 500 B3K A 19 HIS A 20 7 145.96 REMARK 500 B3D A 15 HIS A 16 8 144.30 REMARK 500 B3K A 19 HIS A 20 8 147.25 REMARK 500 B3D A 15 HIS A 16 9 142.56 REMARK 500 B3K A 19 HIS A 20 9 145.94 REMARK 500 B3Q A 25 ASN A 26 9 -144.04 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 1 B3D A 15 -18.87 REMARK 500 1 B3K A 19 -19.05 REMARK 500 1 B3K A 22 -12.87 REMARK 500 2 B3D A 15 -18.96 REMARK 500 2 B3K A 19 -18.99 REMARK 500 2 B3K A 22 -12.70 REMARK 500 2 B3Q A 25 -10.72 REMARK 500 3 B3D A 15 -18.88 REMARK 500 3 B3K A 19 -19.03 REMARK 500 3 B3K A 22 -12.87 REMARK 500 4 B3D A 15 -19.16 REMARK 500 4 B3K A 19 -19.06 REMARK 500 4 B3K A 22 -12.66 REMARK 500 5 B3D A 15 -19.50 REMARK 500 5 B3K A 19 -18.87 REMARK 500 5 B3K A 22 -12.69 REMARK 500 6 B3D A 15 -19.50 REMARK 500 6 B3K A 19 -18.88 REMARK 500 6 B3K A 22 -12.79 REMARK 500 7 B3D A 15 -18.80 REMARK 500 7 B3K A 19 -19.08 REMARK 500 7 B3K A 22 -12.63 REMARK 500 8 B3D A 15 -18.47 REMARK 500 8 B3K A 19 -18.74 REMARK 500 8 B3K A 22 -12.75 REMARK 500 9 B3D A 15 -18.76 REMARK 500 9 B3K A 19 -19.06 REMARK 500 9 B3K A 22 -13.14 REMARK 500 9 B3Q A 25 17.58 REMARK 500 REMARK 500 REMARK: NULL 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 ZN A 101 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 4 SG REMARK 620 2 CYS A 7 SG 109.1 REMARK 620 3 HIS A 20 NE2 118.9 112.0 REMARK 620 4 HIS A 24 NE2 98.0 113.8 104.1 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Ligand residues B3D A 15 REMARK 800 through HIS A 16 bound to SER A 14 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Ligand residues B3K A 19 REMARK 800 through HIS A 20 bound to SER A 18 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 30244 RELATED DB: BMRB REMARK 900 HETEROGENEOUS-BACKBONE FOLDAMER MIMIC OF THE SP1-3 ZINC FINGER DBREF 5US3 A 1 29 PDB 5US3 5US3 1 29 SEQRES 1 A 29 LYS TYR MAA CYS PRO GLU CYS PRO LYS MMO PHE NLE ARG SEQRES 2 A 29 SER B3D HIS LEU SER B3K HIS ILE B3K THR HIS B3Q ASN SEQRES 3 A 29 LYS LYS NH2 HET MAA A 3 13 HET MMO A 10 27 HET NLE A 12 19 HET B3D A 15 15 HET B3K A 19 25 HET B3K A 22 25 HET B3Q A 25 20 HET NH2 A 29 3 HET ZN A 101 1 HETNAM MAA N-METHYL-L-ALANINE HETNAM MMO N~2~-METHYL-L-ARGININE HETNAM NLE NORLEUCINE HETNAM B3D 3-AMINOPENTANEDIOIC ACID HETNAM B3K (3S)-3,7-DIAMINOHEPTANOIC ACID HETNAM B3Q (3S)-3,6-DIAMINO-6-OXOHEXANOIC ACID HETNAM NH2 AMINO GROUP HETNAM ZN ZINC ION HETSYN B3D BETA-HOMOASPARTATE HETSYN B3Q (S)-BETA-3-HOMOGLUTAMINE FORMUL 1 MAA C4 H9 N O2 FORMUL 1 MMO C7 H16 N4 O2 FORMUL 1 NLE C6 H13 N O2 FORMUL 1 B3D C5 H9 N O4 FORMUL 1 B3K 2(C7 H16 N2 O2) FORMUL 1 B3Q C6 H12 N2 O3 FORMUL 1 NH2 H2 N FORMUL 2 ZN ZN 2+ HELIX 1 AA1 ARG A 13 ASN A 26 1 14 LINK C TYR A 2 N MAA A 3 1555 1555 1.39 LINK C MAA A 3 N CYS A 4 1555 1555 1.32 LINK C LYS A 9 N MMO A 10 1555 1555 1.36 LINK C MMO A 10 N PHE A 11 1555 1555 1.31 LINK C PHE A 11 N NLE A 12 1555 1555 1.34 LINK C NLE A 12 N ARG A 13 1555 1555 1.34 LINK C SER A 14 N B3D A 15 1555 1555 1.34 LINK C B3D A 15 N HIS A 16 1555 1555 1.35 LINK C SER A 18 N B3K A 19 1555 1555 1.34 LINK C B3K A 19 N HIS A 20 1555 1555 1.35 LINK C ILE A 21 N B3K A 22 1555 1555 1.33 LINK C B3K A 22 N THR A 23 1555 1555 1.36 LINK C HIS A 24 N B3Q A 25 1555 1555 1.30 LINK C B3Q A 25 N ASN A 26 1555 1555 1.34 LINK C LYS A 28 N NH2 A 29 1555 1555 1.33 LINK SG CYS A 4 ZN ZN A 101 1555 1555 2.24 LINK SG CYS A 7 ZN ZN A 101 1555 1555 2.25 LINK NE2 HIS A 20 ZN ZN A 101 1555 1555 1.94 LINK NE2 HIS A 24 ZN ZN A 101 1555 1555 1.90 SITE 1 AC1 4 CYS A 4 CYS A 7 HIS A 20 HIS A 24 SITE 1 AC2 6 ARG A 13 SER A 14 LEU A 17 SER A 18 SITE 2 AC2 6 B3K A 19 HIS A 20 SITE 1 AC3 13 CYS A 4 CYS A 7 LYS A 9 PHE A 11 SITE 2 AC3 13 B3D A 15 HIS A 16 LEU A 17 SER A 18 SITE 3 AC3 13 ILE A 21 B3K A 22 THR A 23 HIS A 24 SITE 4 AC3 13 ZN A 101 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