10 20 30 40 50 60 70 80 1QP6 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER DE NOVO PROTEIN 01-JUN-99 1QP6
TITLE SOLUTION STRUCTURE OF ALPHA2D
COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (ALPHA2D); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. SOURCE 4 THIS SEQUENCE WAS DESIGNED TO FOLD INTO A HELIX-TURN-HELIX SOURCE 5 PEPTIDE THAT DIMERIZES TO FORM A FOUR-HELIX BUNDLE.
KEYWDS DE NOVO DESIGN, PROTEIN DESIGN, PROTEIN FOLDING, BISECTING KEYWDS 2 U MOTIF, FOUR-HELIX BUNDLE, HELIX-TURN-HELIX, DE NOVO KEYWDS 3 PROTEIN
EXPDTA SOLUTION NMR
NUMMDL 16
AUTHOR R.B.HILL,W.F.DEGRADO
REVDAT 2 24-FEB-09 1QP6 1 VERSN REVDAT 1 09-JUN-99 1QP6 0
JRNL AUTH R.B.HILL,W.F.DEGRADO JRNL TITL SOLUTION STRUCTURE OF ALPHA2D, A NATIVELIKE DE JRNL TITL 2 NOVO DESIGNED PROTEIN JRNL REF J.AM.CHEM.SOC. V. 120 1138 1998 JRNL REFN ISSN 0002-7863 JRNL DOI 10.1021/JA9733649
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH D.P.RALEIGH,S.F.BETZ,W.F.DEGRADO REMARK 1 TITL A DE NOVO DESIGNED PROTEIN MIMICS THE NATIVE STATE REMARK 1 TITL 2 OF NATURAL PROTEINS REMARK 1 REF J.AM.CHEM.SOC. V. 117 7558 1995 REMARK 1 REFN ISSN 0002-7863
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STRUCTURE BASED ON 834 RESTRAINTS: REMARK 3 140 LONG-RANGE RESTRAINTS, 30 PHI ANGLE RESTRAINTS, AND 14 CHI REMARK 3 -1 ANGLE RESTRAINTS. 83 OF THE LONG-RANGE NOES (59%) WERE REMARK 3 DETERMINED TO ARISE FROM INTER-MONOMER CORRELATIONS BY REMARK 3 COMPUTATIONAL METHODS. THE OTHER NOES WERE TREATED USING A REMARK 3 WEIGHTING FUNCTION DEVELOPED FOR SYMMMETRIC HOMODIMERS THAT REMARK 3 ALLOWS EACH NOE TO ARISE FROM EITHER AN INTRA- OR INTER- REMARK 3 MONOMER CORRELATIONS AS DESCRIBED BY NILGES, M. PROTEINS REMARK 3 (1993) 17:297- 309. SYMMETRY TERMS WERE EMPLOYED FOR C-ALPHA REMARK 3 CARBONS ONLY. SEE JACS(1998)120: 1138-1145 FOR MORE DETAILS.
REMARK 4 REMARK 4 1QP6 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-JUN-99. REMARK 100 THE RCSB ID CODE IS RCSB009135.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298.0 REMARK 210 PH : 7.3 REMARK 210 IONIC STRENGTH : 52 MM REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 2 MM ALPHA2D TRIS, PH 7.3, 25 REMARK 210 C REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY, DQF-COSY, E-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR 3.1 REMARK 210 METHOD USED : SIMULATED ANNEALING FOR 48 PS REMARK 210 AT 2000K FOLLOWED BY A SLOW REMARK 210 COOL TO 50K REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 60 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 16 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 11 REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING 2D HOMONUCLEAR REMARK 210 TECHNIQUES. BECAUSE ALPHA2D EXISTS AS A SYMMETRIC HOMODIMER, REMARK 210 THERE EXISTS A PROBLEM OF DETERMINING WHETHER AN OBSERVED NOE REMARK 210 ARISES FROM AN INTER- OR INTRA- MONOMER CORRELATION. THIS REMARK 210 PROBLEM WAS DEALT WITH AS DESCRIBED REMARK 3.
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 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 GLU A 2 -97.58 -133.01 REMARK 500 1 PRO A 17 -157.17 -78.60 REMARK 500 1 ARG A 18 -175.06 -53.32 REMARK 500 1 ARG A 19 -49.64 -147.60 REMARK 500 1 LYS A 34 -174.06 52.21 REMARK 500 1 GLU B 2 -97.62 -132.99 REMARK 500 1 PRO B 17 -157.16 -78.69 REMARK 500 1 ARG B 18 -174.97 -53.26 REMARK 500 1 ARG B 19 -49.61 -147.67 REMARK 500 1 LYS B 34 -174.17 52.11 REMARK 500 2 PRO A 17 -154.78 -76.43 REMARK 500 2 ARG A 18 -175.06 -53.74 REMARK 500 2 ARG A 19 -41.55 -149.92 REMARK 500 2 LYS A 34 95.38 53.18 REMARK 500 2 PRO B 17 -154.86 -76.29 REMARK 500 2 ARG B 18 -174.99 -53.65 REMARK 500 2 ARG B 19 -41.60 -150.06 REMARK 500 2 LYS B 34 95.46 53.23 REMARK 500 3 PRO A 17 -157.78 -77.31 REMARK 500 3 ARG A 18 177.15 -49.62 REMARK 500 3 ARG A 19 -39.38 -143.95 REMARK 500 3 LYS A 34 88.99 52.15 REMARK 500 3 PRO B 17 -157.82 -77.21 REMARK 500 3 ARG B 18 177.26 -49.60 REMARK 500 3 ARG B 19 -39.30 -144.05 REMARK 500 3 LYS B 34 88.95 52.12 REMARK 500 4 LYS A 15 74.55 -102.23 REMARK 500 4 PRO A 17 -159.13 -77.08 REMARK 500 4 ARG A 18 171.80 -47.91 REMARK 500 4 ARG A 19 -43.22 -139.06 REMARK 500 4 LYS A 34 74.83 54.12 REMARK 500 4 LYS B 15 74.61 -102.51 REMARK 500 4 PRO B 17 -159.08 -77.07 REMARK 500 4 ARG B 18 171.74 -47.82 REMARK 500 4 ARG B 19 -43.25 -139.11 REMARK 500 4 LYS B 34 74.63 54.42 REMARK 500 5 LYS A 15 76.44 -102.56 REMARK 500 5 PRO A 17 -158.21 -77.19 REMARK 500 5 ARG A 18 174.24 -48.82 REMARK 500 5 ARG A 19 -40.04 -139.43 REMARK 500 5 LYS B 15 76.44 -102.52 REMARK 500 5 PRO B 17 -158.16 -77.24 REMARK 500 5 ARG B 18 174.20 -48.88 REMARK 500 5 ARG B 19 -40.09 -139.41 REMARK 500 6 LYS A 15 61.82 -103.35 REMARK 500 6 PRO A 17 -90.47 -74.40 REMARK 500 6 LYS A 34 87.58 55.11 REMARK 500 6 LYS B 15 62.01 -103.26 REMARK 500 6 PRO B 17 -90.43 -74.36 REMARK 500 6 LYS B 34 87.45 55.08 REMARK 500 7 PRO A 17 -159.36 -76.49 REMARK 500 7 ARG A 18 175.24 -49.38 REMARK 500 7 ARG A 19 -40.09 -140.22 REMARK 500 7 PRO B 17 -159.15 -76.45 REMARK 500 7 ARG B 18 175.29 -49.57 REMARK 500 7 ARG B 19 -40.13 -140.28 REMARK 500 8 GLU A 2 19.24 -152.66 REMARK 500 8 PRO A 17 -157.64 -76.95 REMARK 500 8 ARG A 18 174.09 -48.43 REMARK 500 8 ARG A 19 -40.94 -140.78 REMARK 500 8 LYS A 34 179.28 52.27 REMARK 500 8 GLU B 2 19.62 -152.78 REMARK 500 8 PRO B 17 -157.69 -77.00 REMARK 500 8 ARG B 18 174.16 -48.55 REMARK 500 8 ARG B 19 -40.84 -140.81 REMARK 500 8 LYS B 34 179.20 52.49 REMARK 500 9 PRO A 17 -160.72 -77.79 REMARK 500 9 ARG A 18 170.04 -48.42 REMARK 500 9 ARG A 19 -39.90 -137.08 REMARK 500 9 PRO B 17 -160.72 -77.83 REMARK 500 9 ARG B 18 170.10 -48.34 REMARK 500 9 ARG B 19 -39.70 -137.20 REMARK 500 10 GLU A 2 -68.51 -99.93 REMARK 500 10 LYS A 15 71.92 -102.43 REMARK 500 10 PRO A 17 -159.83 -77.26 REMARK 500 10 ARG A 18 170.56 -47.74 REMARK 500 10 ARG A 19 -38.63 -137.69 REMARK 500 10 GLU B 2 -68.49 -100.00 REMARK 500 10 LYS B 15 71.71 -102.32 REMARK 500 10 PRO B 17 -159.81 -77.20 REMARK 500 10 ARG B 18 170.68 -47.69 REMARK 500 10 ARG B 19 -38.68 -137.77 REMARK 500 11 LYS A 15 70.43 -104.13 REMARK 500 11 PRO A 17 -158.06 -77.51 REMARK 500 11 ARG A 18 171.64 -47.99 REMARK 500 11 ARG A 19 -50.63 -139.05 REMARK 500 11 LYS B 15 70.40 -104.10 REMARK 500 11 PRO B 17 -158.08 -77.51 REMARK 500 11 ARG B 18 171.77 -47.98 REMARK 500 11 ARG B 19 -50.52 -139.24 REMARK 500 12 GLU A 2 -66.57 -136.94 REMARK 500 12 VAL A 3 -37.45 -170.57 REMARK 500 12 PRO A 17 -158.90 -79.12 REMARK 500 12 ARG A 18 -178.04 -50.33 REMARK 500 12 ARG A 19 -52.89 -151.94 REMARK 500 12 GLU B 2 -66.86 -137.03 REMARK 500 12 VAL B 3 -36.90 -170.57 REMARK 500 12 PRO B 17 -158.99 -79.12 REMARK 500 12 ARG B 18 -177.95 -50.23 REMARK 500 12 ARG B 19 -52.69 -152.03 REMARK 500 13 GLU A 2 17.13 56.21 REMARK 500 13 LYS A 15 73.54 -103.00 REMARK 500 13 PRO A 17 -158.83 -77.68 REMARK 500 13 ARG A 18 175.57 -49.22 REMARK 500 13 ARG A 19 -38.32 -139.58 REMARK 500 13 GLU B 2 17.29 56.20 REMARK 500 13 LYS B 15 73.71 -102.92 REMARK 500 13 PRO B 17 -158.86 -77.63 REMARK 500 13 ARG B 18 175.39 -49.27 REMARK 500 13 ARG B 19 -38.44 -139.32 REMARK 500 14 LYS A 15 79.45 -104.48 REMARK 500 14 PRO A 17 -158.51 -78.35 REMARK 500 14 ARG A 18 173.53 -48.94 REMARK 500 14 ARG A 19 -41.06 -140.62 REMARK 500 14 LYS B 15 79.49 -104.55 REMARK 500 14 PRO B 17 -158.60 -78.17 REMARK 500 14 ARG B 18 173.52 -48.91 REMARK 500 14 ARG B 19 -40.94 -140.67 REMARK 500 15 PRO A 17 -159.10 -76.78 REMARK 500 15 ARG A 18 172.40 -48.28 REMARK 500 15 ARG A 19 -41.12 -140.78 REMARK 500 15 LYS A 34 82.62 51.44 REMARK 500 15 PRO B 17 -158.96 -76.80 REMARK 500 15 ARG B 18 172.50 -48.38 REMARK 500 15 ARG B 19 -41.10 -140.86 REMARK 500 15 LYS B 34 82.64 51.57 REMARK 500 16 GLU A 2 85.47 53.51 REMARK 500 16 VAL A 3 36.02 37.81 REMARK 500 16 PRO A 17 -158.01 -77.94 REMARK 500 16 ARG A 18 175.79 -49.61 REMARK 500 16 ARG A 19 -45.01 -141.44 REMARK 500 16 LYS A 34 -179.62 53.22 REMARK 500 16 GLU B 2 85.65 53.38 REMARK 500 16 VAL B 3 36.22 37.59 REMARK 500 16 PRO B 17 -158.10 -77.88 REMARK 500 16 ARG B 18 175.75 -49.67 REMARK 500 16 ARG B 19 -44.92 -141.42 REMARK 500 16 LYS B 34 -179.67 53.22 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 1 ARG A 18 0.10 SIDE_CHAIN REMARK 500 1 ARG A 19 0.31 SIDE_CHAIN REMARK 500 1 ARG B 18 0.10 SIDE_CHAIN REMARK 500 1 ARG B 19 0.31 SIDE_CHAIN REMARK 500 2 ARG A 18 0.24 SIDE_CHAIN REMARK 500 2 ARG A 19 0.31 SIDE_CHAIN REMARK 500 2 ARG B 18 0.24 SIDE_CHAIN REMARK 500 2 ARG B 19 0.31 SIDE_CHAIN REMARK 500 3 ARG A 18 0.27 SIDE_CHAIN REMARK 500 3 ARG A 19 0.31 SIDE_CHAIN REMARK 500 3 ARG B 18 0.27 SIDE_CHAIN REMARK 500 3 ARG B 19 0.31 SIDE_CHAIN REMARK 500 4 ARG A 18 0.17 SIDE_CHAIN REMARK 500 4 ARG A 19 0.32 SIDE_CHAIN REMARK 500 4 ARG B 18 0.17 SIDE_CHAIN REMARK 500 4 ARG B 19 0.32 SIDE_CHAIN REMARK 500 5 ARG A 18 0.26 SIDE_CHAIN REMARK 500 5 ARG A 19 0.30 SIDE_CHAIN REMARK 500 5 ARG B 18 0.26 SIDE_CHAIN REMARK 500 5 ARG B 19 0.30 SIDE_CHAIN REMARK 500 6 ARG A 18 0.23 SIDE_CHAIN REMARK 500 6 ARG A 19 0.30 SIDE_CHAIN REMARK 500 6 ARG B 18 0.23 SIDE_CHAIN REMARK 500 6 ARG B 19 0.30 SIDE_CHAIN REMARK 500 7 ARG A 18 0.25 SIDE_CHAIN REMARK 500 7 ARG A 19 0.15 SIDE_CHAIN REMARK 500 7 ARG B 18 0.25 SIDE_CHAIN REMARK 500 7 ARG B 19 0.15 SIDE_CHAIN REMARK 500 8 ARG A 18 0.24 SIDE_CHAIN REMARK 500 8 ARG A 19 0.30 SIDE_CHAIN REMARK 500 8 ARG B 18 0.24 SIDE_CHAIN REMARK 500 8 ARG B 19 0.30 SIDE_CHAIN REMARK 500 9 ARG A 18 0.26 SIDE_CHAIN REMARK 500 9 ARG A 19 0.26 SIDE_CHAIN REMARK 500 9 ARG B 18 0.26 SIDE_CHAIN REMARK 500 9 ARG B 19 0.26 SIDE_CHAIN REMARK 500 10 ARG A 18 0.26 SIDE_CHAIN REMARK 500 10 ARG A 19 0.30 SIDE_CHAIN REMARK 500 10 ARG B 18 0.26 SIDE_CHAIN REMARK 500 10 ARG B 19 0.30 SIDE_CHAIN REMARK 500 11 ARG A 18 0.19 SIDE_CHAIN REMARK 500 11 ARG A 19 0.22 SIDE_CHAIN REMARK 500 11 ARG B 18 0.19 SIDE_CHAIN REMARK 500 11 ARG B 19 0.22 SIDE_CHAIN REMARK 500 12 ARG A 18 0.32 SIDE_CHAIN REMARK 500 12 ARG A 19 0.22 SIDE_CHAIN REMARK 500 12 ARG B 18 0.32 SIDE_CHAIN REMARK 500 12 ARG B 19 0.22 SIDE_CHAIN REMARK 500 13 ARG A 18 0.14 SIDE_CHAIN REMARK 500 13 ARG A 19 0.25 SIDE_CHAIN REMARK 500 13 ARG B 18 0.14 SIDE_CHAIN REMARK 500 13 ARG B 19 0.25 SIDE_CHAIN REMARK 500 14 ARG A 18 0.22 SIDE_CHAIN REMARK 500 14 ARG A 19 0.23 SIDE_CHAIN REMARK 500 14 ARG B 18 0.22 SIDE_CHAIN REMARK 500 14 ARG B 19 0.23 SIDE_CHAIN REMARK 500 15 ARG A 18 0.14 SIDE_CHAIN REMARK 500 15 ARG A 19 0.32 SIDE_CHAIN REMARK 500 15 ARG B 18 0.14 SIDE_CHAIN REMARK 500 15 ARG B 19 0.32 SIDE_CHAIN REMARK 500 16 ARG A 18 0.12 SIDE_CHAIN REMARK 500 16 ARG A 19 0.26 SIDE_CHAIN REMARK 500 16 ARG B 18 0.12 SIDE_CHAIN REMARK 500 16 ARG B 19 0.26 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL
DBREF 1QP6 A 1 35 PDB 1QP6 1QP6 1 35 DBREF 1QP6 B 1 35 PDB 1QP6 1QP6 1 35
SEQRES 1 A 35 GLY GLU VAL GLU GLU LEU GLU LYS LYS PHE LYS GLU LEU SEQRES 2 A 35 TRP LYS GLY PRO ARG ARG GLY GLU ILE GLU GLU LEU HIS SEQRES 3 A 35 LYS LYS PHE HIS GLU LEU ILE LYS GLY SEQRES 1 B 35 GLY GLU VAL GLU GLU LEU GLU LYS LYS PHE LYS GLU LEU SEQRES 2 B 35 TRP LYS GLY PRO ARG ARG GLY GLU ILE GLU GLU LEU HIS SEQRES 3 B 35 LYS LYS PHE HIS GLU LEU ILE LYS GLY
HELIX 1 1 VAL A 3 LYS A 15 1 13 HELIX 2 2 ARG A 19 LYS A 34 1 16 HELIX 3 3 VAL B 3 LYS B 15 1 13 HELIX 4 4 ARG B 19 LYS B 34 1 16
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