SMTL ID : 6oad.1 (1 other biounit)

2.05 Angstrom Resolution Crystal Structure of Aminopeptidase B from Escherichia coli str. K-12 substr. MG1655.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-hexamer

Ligands

12 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: K.198, D.203, D.221, E.282 Ligands: ZN.2, BCT.5 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.203, A:D.221, A:D.221, A:E.282, H2O.8 ZN.2: 5 residues within 4Å: Chain A: D.203, K.210, D.280, E.282 Ligands: ZN.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.203, A:D.280, A:D.280, A:E.282, H2O.8 ZN.10: 6 residues within 4Å: Chain B: K.198, D.203, D.221, E.282 Ligands: ZN.11, BCT.14 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.203, B:D.221, B:D.221, B:E.282, H2O.18 ZN.11: 4 residues within 4Å: Chain B: D.203, D.280, E.282 Ligands: ZN.10 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.203, B:D.280, B:D.280, B:E.282, H2O.18 ZN.18: 6 residues within 4Å: Chain C: K.198, D.203, D.221, E.282 Ligands: ZN.19, BCT.22 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.203, C:D.221, C:E.282, H2O.27 ZN.19: 5 residues within 4Å: Chain C: D.203, K.210, D.280, E.282 Ligands: ZN.18 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.203, C:D.280, C:D.280, C:E.282, H2O.27 ZN.28: 6 residues within 4Å: Chain D: K.198, D.203, D.221, E.282 Ligands: ZN.29, BCT.31 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.203, D:D.221, D:D.221, D:E.282, H2O.37 ZN.29: 5 residues within 4Å: Chain D: D.203, D.280, E.282 Ligands: ZN.28, EDO.35 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.203, D:D.280, D:D.280, D:E.282, H2O.37 ZN.39: 6 residues within 4Å: Chain E: K.198, D.203, D.221, E.282 Ligands: ZN.40, BCT.43 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.203, E:D.221, E:E.282, H2O.48 ZN.40: 4 residues within 4Å: Chain E: D.203, D.280, E.282 Ligands: ZN.39 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.203, E:D.280, E:D.280, E:E.282, H2O.48 ZN.48: 6 residues within 4Å: Chain F: K.198, D.203, D.221, E.282 Ligands: ZN.49, BCT.52 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.203, F:D.221, F:D.221, F:E.282, H2O.52 ZN.49: 5 residues within 4Å: Chain F: D.203, D.280, E.282 Ligands: ZN.48, EDO.54 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.203, F:D.280, F:D.280, F:E.282, H2O.52

6 x CA: CALCIUM ION(Non-covalent)

CA.3: 6 residues within 4Å: Chain A: T.116, I.117, A.119, L.124, K.219, M.222 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:I.117, A:A.119, A:K.219, H2O.4 CA.12: 6 residues within 4Å: Chain B: T.116, I.117, A.119, L.124, K.219, M.222 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:I.117, B:A.119, B:K.219, H2O.18 CA.20: 6 residues within 4Å: Chain C: T.116, I.117, A.119, L.124, K.219, M.222 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:I.117, C:A.119, C:K.219, H2O.25 CA.30: 6 residues within 4Å: Chain D: T.116, I.117, A.119, L.124, K.219, M.222 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:I.117, D:A.119, D:K.219, H2O.37 CA.41: 6 residues within 4Å: Chain E: T.116, I.117, A.119, L.124, K.219, M.222 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:I.117, E:A.119, E:K.219, H2O.46 CA.50: 6 residues within 4Å: Chain F: T.116, I.117, A.119, L.124, K.219, M.222 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:I.117, F:A.119, F:K.219, H2O.55

6 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 3 residues within 4Å: Chain A: K.272, R.355, H.386 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain B: K.272, R.355, H.386 Ligand excluded by PLIP CL.17: 2 residues within 4Å: Chain B: R.88, V.90 Ligand excluded by PLIP CL.21: 3 residues within 4Å: Chain C: K.151, R.172, S.173 Ligand excluded by PLIP CL.42: 4 residues within 4Å: Chain E: D.70, A.71, D.72, Q.99 Ligand excluded by PLIP CL.51: 4 residues within 4Å: Chain F: K.151, E.171, R.172, S.173 Ligand excluded by PLIP

10 x BCT: BICARBONATE ION(Non-functional Binders)

BCT.5: 9 residues within 4Å: Chain A: K.198, D.280, A.281, E.282, G.283, R.284, L.308 Ligands: ZN.1, PGE.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.284, A:R.284, A:L.308 BCT.14: 8 residues within 4Å: Chain B: K.198, D.280, A.281, E.282, G.283, R.284, L.308 Ligands: ZN.10 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.284, B:R.284, B:L.308 BCT.22: 8 residues within 4Å: Chain C: K.198, D.280, A.281, E.282, G.283, R.284, L.308 Ligands: ZN.18 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.284, C:R.284, C:L.308 Water bridges: C:K.198 BCT.23: 2 residues within 4Å: Chain C: D.154, E.157 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.154 BCT.31: 9 residues within 4Å: Chain D: K.198, D.280, A.281, E.282, G.283, R.284, L.308 Ligands: ZN.28, PEG.38 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:A.281, D:G.283, D:R.284, D:L.308 BCT.32: 7 residues within 4Å: Chain D: R.355, S.356, Q.357, L.358, P.359, E.364, L.365 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:L.358 Water bridges: D:S.360 BCT.33: 4 residues within 4Å: Chain D: K.151, E.171, R.172, S.173 2 PLIP interactions: 2 interactions with chain D Water bridges: D:K.151, D:S.173 BCT.43: 8 residues within 4Å: Chain E: K.198, D.280, A.281, E.282, G.283, R.284, L.308 Ligands: ZN.39 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:A.281, E:G.283, E:R.284, E:L.308 Water bridges: E:K.198 BCT.52: 8 residues within 4Å: Chain F: K.198, D.280, A.281, E.282, G.283, R.284, L.308 Ligands: ZN.48 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:E.282, F:G.283, F:R.284, F:R.284, F:R.284 BCT.53: 3 residues within 4Å: Chain F: T.309, G.310, A.311 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:G.310

17 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.6: 7 residues within 4Å: Chain A: Q.48, W.75, Q.79, E.341, N.342, L.419, R.422 Ligand excluded by PLIP EDO.7: 1 residues within 4Å: Chain A: E.157 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain A: W.78, R.88, K.89, V.90, W.92 Ligand excluded by PLIP EDO.15: 7 residues within 4Å: Chain B: Q.48, W.75, Q.79, E.341, N.342, L.419, R.422 Ligand excluded by PLIP EDO.16: 4 residues within 4Å: Chain B: K.151, E.171, R.172, S.173 Ligand excluded by PLIP EDO.24: 7 residues within 4Å: Chain C: W.75, Q.79, E.341, N.342, E.343, L.419, R.422 Ligand excluded by PLIP EDO.25: 7 residues within 4Å: Chain C: P.299, E.300, I.302, V.388, N.390, Q.393, G.394 Ligand excluded by PLIP EDO.27: 6 residues within 4Å: Chain C: W.78, R.88, K.89, V.90, W.92, L.107 Ligand excluded by PLIP EDO.34: 6 residues within 4Å: Chain D: W.75, Q.79, E.341, N.342, L.419, R.422 Ligand excluded by PLIP EDO.35: 9 residues within 4Å: Chain D: D.203, K.210, M.218, D.221, T.307, L.308, K.313 Ligands: ZN.29, PEG.38 Ligand excluded by PLIP EDO.36: 5 residues within 4Å: Chain D: W.78, R.88, K.89, V.90, W.92 Ligand excluded by PLIP EDO.44: 4 residues within 4Å: Chain E: S.127, K.151, R.172, S.173 Ligand excluded by PLIP EDO.45: 6 residues within 4Å: Chain E: Q.48, W.75, Q.79, N.342, L.419, R.422 Ligand excluded by PLIP EDO.46: 5 residues within 4Å: Chain E: W.78, R.88, K.89, V.90, W.92 Ligand excluded by PLIP EDO.54: 9 residues within 4Å: Chain F: D.203, K.210, M.218, D.280, T.307, L.308, T.309, K.313 Ligands: ZN.49 Ligand excluded by PLIP EDO.55: 6 residues within 4Å: Chain F: Q.48, W.75, Q.79, E.341, N.342, R.422 Ligand excluded by PLIP EDO.56: 5 residues within 4Å: Chain F: W.78, R.88, K.89, V.90, W.92 Ligand excluded by PLIP

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.9: 9 residues within 4Å: Chain A: N.278, D.280, A.281, L.308, T.309, G.310, A.311, T.368 Ligands: BCT.5 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.310, A:A.311, A:T.368 Water bridges: A:R.284, A:R.284

4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.26: 4 residues within 4Å: Chain C: E.389, N.390, Y.391, Q.392 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.390, C:Q.392, C:Q.392 PEG.37: 9 residues within 4Å: Chain D: S.295, P.299, E.300, I.302, V.388, E.389, N.390, Q.393, G.394 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:P.299, D:N.390 PEG.38: 7 residues within 4Å: Chain D: D.280, T.309, G.310, A.311, G.376 Ligands: BCT.31, EDO.35 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:A.281, D:G.310, D:A.311 PEG.47: 6 residues within 4Å: Chain E: D.280, A.281, L.308, T.309, G.310, A.311 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:G.310, E:A.311 Water bridges: E:R.284

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Minasov, G. et al., Comparison of metal-bound and unbound structures of aminopeptidase B proteins from Escherichia coli and Yersinia pestis. Protein Sci. (2020)

Release Date

2019-03-27

Peptides

Peptidase B: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Peptidase B

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