SMTL ID : 6oad.2 (1 other biounit)

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

Coordinates

PDB Format Compare

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.4 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.3 ZN.2: 4 residues within 4Å: Chain A: D.203, 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.3 ZN.9: 6 residues within 4Å: Chain B: K.198, D.203, D.221, E.282 Ligands: ZN.10, BCT.12 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.10: 5 residues within 4Å: Chain B: D.203, K.210, D.280, E.282 Ligands: ZN.9 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.19: 6 residues within 4Å: Chain C: K.198, D.203, D.221, E.282 Ligands: ZN.20, BCT.24 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.203, C:D.221, C:E.282, H2O.31 ZN.20: 5 residues within 4Å: Chain C: D.203, K.210, D.280, E.282 Ligands: ZN.19 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.31 ZN.28: 7 residues within 4Å: Chain D: K.198, D.203, D.221, E.282 Ligands: ZN.29, BCT.31, EDO.33 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.38 ZN.29: 5 residues within 4Å: Chain D: D.203, D.280, E.282 Ligands: ZN.28, EDO.33 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.38 ZN.37: 6 residues within 4Å: Chain E: K.198, D.203, D.221, E.282 Ligands: ZN.38, BCT.41 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.203, E:D.221, E:E.282, H2O.49 ZN.38: 4 residues within 4Å: Chain E: D.203, D.280, E.282 Ligands: ZN.37 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.49 ZN.45: 7 residues within 4Å: Chain F: K.198, D.203, D.221, E.282 Ligands: ZN.46, BCT.50, EDO.52 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.203, F:D.221, F:E.282, H2O.58 ZN.46: 5 residues within 4Å: Chain F: D.203, D.280, E.282 Ligands: ZN.45, EDO.52 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.58

7 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.6 CA.11: 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.17 CA.21: 6 residues within 4Å: Chain C: T.116, I.117, A.119, L.124, K.219, M.222 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:T.116, C:I.117, C:A.119, C:K.219, H2O.31 CA.22: 2 residues within 4Å: Chain C: D.154, E.157 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.154, C:E.157, C:E.157, H2O.33 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.40 CA.39: 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.53 CA.47: 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.66

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

BCT.4: 8 residues within 4Å: Chain A: K.198, D.280, A.281, E.282, G.283, R.284, L.308 Ligands: ZN.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.284, A:R.284, A:L.308 BCT.5: 7 residues within 4Å: Chain A: P.299, E.300, I.302, V.388, N.390, Q.393, G.394 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.394 Water bridges: A:N.390 BCT.12: 8 residues within 4Å: Chain B: K.198, D.280, A.281, E.282, G.283, R.284, L.308 Ligands: ZN.9 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.284, B:R.284, B:L.308 BCT.23: 3 residues within 4Å: Chain C: R.156, E.157, G.159 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.157 BCT.24: 8 residues within 4Å: Chain C: K.198, D.280, A.281, E.282, G.283, R.284, L.308 Ligands: ZN.19 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.284, C:R.284, C:L.308 BCT.31: 8 residues within 4Å: Chain D: K.198, D.280, A.281, E.282, G.283, R.284, L.308 Ligands: ZN.28 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:E.282, D:G.283, D:R.284, D:R.284, D:R.284 BCT.41: 8 residues within 4Å: Chain E: K.198, D.280, A.281, E.282, G.283, R.284, L.308 Ligands: ZN.37 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:A.281, E:G.283, E:R.284, E:L.308 BCT.42: 6 residues within 4Å: Chain E: P.299, I.302, V.388, N.390, Q.393, G.394 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:P.299, E:N.390 Water bridges: E:N.390 BCT.50: 8 residues within 4Å: Chain F: K.198, D.280, A.281, E.282, G.283, R.284, L.308 Ligands: ZN.45 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:A.281, F:G.283, F:R.284, F:L.308 Water bridges: F:K.198

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

EDO.6: 6 residues within 4Å: Chain A: Q.48, W.75, Q.79, N.342, L.419, R.422 Ligand excluded by PLIP EDO.7: 7 residues within 4Å: Chain A: E.171 Chain C: R.168, G.169, S.170, E.171, S.256, N.258 Ligand excluded by PLIP EDO.8: 6 residues within 4Å: Chain A: W.78, R.88, K.89, V.90, W.92, L.107 Ligand excluded by PLIP EDO.13: 6 residues within 4Å: Chain B: Q.48, W.75, Q.79, E.341, N.342, R.422 Ligand excluded by PLIP EDO.14: 3 residues within 4Å: Chain B: G.332, R.333, A.336 Ligand excluded by PLIP EDO.15: 6 residues within 4Å: Chain B: P.299, I.302, V.388, N.390, Q.393, G.394 Ligand excluded by PLIP EDO.16: 4 residues within 4Å: Chain B: E.389, N.390, Y.391, Q.392 Ligand excluded by PLIP EDO.17: 2 residues within 4Å: Chain B: T.146, Y.147 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain B: W.78, R.88, K.89, V.90, W.92 Ligand excluded by PLIP EDO.25: 6 residues within 4Å: Chain C: Q.48, W.75, Q.79, N.342, L.419, R.422 Ligand excluded by PLIP EDO.26: 5 residues within 4Å: Chain C: W.78, R.88, K.89, V.90, W.92 Ligand excluded by PLIP EDO.27: 6 residues within 4Å: Chain C: P.299, I.302, V.388, N.390, Q.393, G.394 Ligand excluded by PLIP EDO.32: 6 residues within 4Å: Chain D: W.75, Q.79, E.341, N.342, E.343, R.422 Ligand excluded by PLIP EDO.33: 10 residues within 4Å: Chain D: D.203, K.210, D.221, D.280, T.307, L.308, T.309, K.313 Ligands: ZN.28, ZN.29 Ligand excluded by PLIP EDO.34: 6 residues within 4Å: Chain D: P.299, I.302, V.388, N.390, Q.393, G.394 Ligand excluded by PLIP EDO.35: 5 residues within 4Å: Chain D: W.78, K.82, L.107, D.111, D.115 Ligand excluded by PLIP EDO.36: 6 residues within 4Å: Chain D: W.78, R.88, K.89, V.90, W.92, L.107 Ligand excluded by PLIP EDO.43: 6 residues within 4Å: Chain E: Q.48, W.75, Q.79, E.341, N.342, R.422 Ligand excluded by PLIP EDO.44: 5 residues within 4Å: Chain E: W.78, R.88, K.89, V.90, W.92 Ligand excluded by PLIP EDO.51: 6 residues within 4Å: Chain F: Q.48, W.75, Q.79, N.342, L.419, R.422 Ligand excluded by PLIP EDO.52: 8 residues within 4Å: Chain F: D.203, K.210, M.218, D.280, T.307, L.308 Ligands: ZN.45, ZN.46 Ligand excluded by PLIP EDO.54: 5 residues within 4Å: Chain F: W.78, R.88, K.89, V.90, W.92 Ligand excluded by PLIP

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

CL.40: 3 residues within 4Å: Chain E: K.272, R.355, H.386 Ligand excluded by PLIP CL.48: 3 residues within 4Å: Chain F: T.309, G.310, A.311 Ligand excluded by PLIP CL.49: 3 residues within 4Å: Chain F: K.151, R.172, S.173 Ligand excluded by PLIP

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

PEG.53: 3 residues within 4Å: Chain F: Q.128, Q.131, R.132 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:Q.128, F:R.132, F:R.132

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
G

B
H

C
I

D
J

E
K

F
L

Peptidase B

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