SMTL ID : 1xoc.2 (2 other biounits)

The structure of the oligopeptide-binding protein, AppA, from Bacillus subtilis in complex with a nonapeptide.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-dimer

Ligands

2 x VAL- ASP- SER- LYS- ASN- THR- SER- SER- TRP: Nonapeptide VDSKNTSSW(Non-covalent)

VAL-ASP-SER-LYS-ASN-THR-SER-SER-TRP.1: 35 residues within 4Å: Chain A: I.29, T.41, D.42, D.43, T.46, R.119, T.122, N.150, N.151, D.154, S.155, N.241, A.263, S.265, V.267, N.367, N.370, V.372, R.373, W.398, M.405, N.406, G.418, W.419, S.420, S.422, T.423, I.430, Y.442, Y.487, P.489, N.490, N.491, K.507, R.508 41 PLIP interactions: 41 interactions with chain A Hydrophobic interactions: A:D.154, A:A.263, A:W.398, A:T.423, A:P.489, A:P.489, A:K.507 Hydrogen bonds: A:T.41, A:T.41, A:D.43, A:R.119, A:R.119, A:T.122, A:D.154, A:S.155, A:S.155, A:N.241, A:N.367, A:N.370, A:R.373, A:R.373, A:R.373, A:N.406, A:G.418, A:G.418, A:S.420, A:S.420, A:S.422, A:T.423, A:Y.442, A:Y.442, A:Y.487, A:Y.487, A:K.507, A:K.507, A:R.508 Water bridges: A:S.155, A:T.423, A:D.429, A:D.429 Salt bridges: A:R.119 VAL-ASP-SER-LYS-ASN-THR-SER-SER-TRP.17: 35 residues within 4Å: Chain B: I.29, T.41, D.42, D.43, T.46, R.119, T.122, N.150, N.151, D.154, S.155, N.241, A.263, S.265, V.267, N.367, N.370, V.372, R.373, W.398, M.405, N.406, G.418, W.419, S.420, S.422, T.423, I.430, Y.442, Y.487, P.489, N.490, N.491, K.507, R.508 40 PLIP interactions: 40 interactions with chain B Hydrophobic interactions: B:D.154, B:A.263, B:W.398, B:T.423, B:P.489, B:P.489, B:K.507 Hydrogen bonds: B:T.41, B:T.41, B:D.43, B:R.119, B:R.119, B:T.122, B:D.154, B:S.155, B:S.155, B:N.241, B:N.367, B:N.370, B:R.373, B:R.373, B:R.373, B:N.406, B:G.418, B:G.418, B:S.420, B:S.420, B:S.422, B:T.423, B:Y.442, B:Y.442, B:Y.487, B:K.507, B:K.507, B:R.508 Water bridges: B:S.155, B:T.423, B:D.429, B:D.429 Salt bridges: B:R.119

30 x ZN: ZINC ION(Non-covalent)

ZN.2: 3 residues within 4Å: Chain A: E.97, D.102, H.162 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:H.162, H2O.3, H2O.4, H2O.7, H2O.10 ZN.3: 1 residues within 4Å: Chain A: D.205 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.205, A:D.205, H2O.2 ZN.4: 3 residues within 4Å: Chain A: T.260, D.304, H.492 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.304, A:D.304, A:H.492 ZN.5: 1 residues within 4Å: Chain A: E.374 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.374, A:E.374, H2O.5, H2O.11 ZN.6: 4 residues within 4Å: Chain A: E.130, K.132, K.140 Ligands: ZN.16 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.130, A:E.130, H2O.11, H2O.12 ZN.7: 1 residues within 4Å: Chain A: D.171 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.171 ZN.8: 1 residues within 4Å: Chain A: E.306 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.306, A:E.306 ZN.9: 1 residues within 4Å: Chain A: D.375 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.375, A:D.375 ZN.10: 4 residues within 4Å: Chain A: E.449 Chain B: E.449, K.476 Ligands: ZN.26 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:E.449, A:E.449, B:E.449, H2O.17, H2O.34 ZN.11: 1 residues within 4Å: Chain A: E.118 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.118, H2O.5, H2O.11, H2O.12, H2O.15 ZN.12: 5 residues within 4Å: Chain A: D.346, N.348, D.350, I.352, D.354 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.350, A:D.350, A:I.352, A:D.354, A:D.354 ZN.13: 1 residues within 4Å: Chain A: D.134 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.134, A:D.134 ZN.14: 3 residues within 4Å: Chain A: D.43, D.47, D.509 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.47, H2O.3, H2O.16, H2O.16, H2O.17 ZN.15: 1 residues within 4Å: Chain A: D.224 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.224, H2O.6 ZN.16: 3 residues within 4Å: Chain A: E.130, K.140 Ligands: ZN.6 No protein-ligand interaction detected (PLIP) ZN.18: 3 residues within 4Å: Chain B: E.97, D.102, H.162 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:H.162, H2O.20, H2O.21, H2O.24, H2O.27 ZN.19: 1 residues within 4Å: Chain B: D.205 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.205, B:D.205, H2O.19 ZN.20: 3 residues within 4Å: Chain B: T.260, D.304, H.492 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.304, B:D.304, B:H.492 ZN.21: 1 residues within 4Å: Chain B: E.374 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.374, B:E.374, H2O.22, H2O.28 ZN.22: 4 residues within 4Å: Chain B: E.130, K.132, K.140 Ligands: ZN.32 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.130, B:E.130, H2O.27, H2O.29 ZN.23: 1 residues within 4Å: Chain B: D.171 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.171 ZN.24: 1 residues within 4Å: Chain B: E.306 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.306, B:E.306 ZN.25: 1 residues within 4Å: Chain B: D.375 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.375, B:D.375 ZN.26: 4 residues within 4Å: Chain A: E.449, K.476 Chain B: E.449 Ligands: ZN.10 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:E.449, B:E.449, A:E.449, H2O.17, H2O.34 ZN.27: 1 residues within 4Å: Chain B: E.118 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:E.118, H2O.22, H2O.28, H2O.29, H2O.32 ZN.28: 5 residues within 4Å: Chain B: D.346, N.348, D.350, I.352, D.354 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.350, B:D.350, B:I.352, B:D.354, B:D.354 ZN.29: 1 residues within 4Å: Chain B: D.134 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.134, B:D.134 ZN.30: 3 residues within 4Å: Chain B: D.43, D.47, D.509 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.47, H2O.20, H2O.33, H2O.33, H2O.33 ZN.31: 1 residues within 4Å: Chain B: D.224 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.224, H2O.23 ZN.32: 3 residues within 4Å: Chain B: E.130, K.140 Ligands: ZN.22 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Levdikov, V.M. et al., The structure of the oligopeptide-binding protein, AppA, from Bacillus subtilis in complex with a nonapeptide. J.Mol.Biol. (2005)

Release Date

2005-01-25

Peptides

Oligopeptide-binding protein appA: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Oligopeptide-binding protein appA

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