SMTL ID : 6ov8.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.61 Å

Oligo State

homo-hexamer

Ligands

6 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: K.198, D.203, D.221, E.282 Ligands: MN.2 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.7: 5 residues within 4Å: Chain B: K.198, D.203, D.221, E.282 Ligands: MN.8 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.9 ZN.13: 5 residues within 4Å: Chain C: K.198, D.203, D.221, E.282 Ligands: MN.14 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.203, C:D.221, C:D.221, C:E.282, H2O.13 ZN.18: 5 residues within 4Å: Chain D: K.198, D.203, D.221, E.282 Ligands: MN.19 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.203, D:D.221, D:E.282, H2O.17 ZN.23: 5 residues within 4Å: Chain E: K.198, D.203, D.221, E.282 Ligands: MN.24 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.203, E:D.221, E:E.282, H2O.19, H2O.21 ZN.28: 5 residues within 4Å: Chain F: K.198, D.203, D.221, E.282 Ligands: MN.29 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:D.221, F:D.221, F:E.282, H2O.22, H2O.24

6 x MN: MANGANESE (II) ION(Non-covalent)

MN.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.3 MN.8: 5 residues within 4Å: Chain B: D.203, K.210, D.280, E.282 Ligands: ZN.7 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.9 MN.14: 4 residues within 4Å: Chain C: D.203, D.280, E.282 Ligands: ZN.13 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.13 MN.19: 5 residues within 4Å: Chain D: D.203, K.210, D.280, E.282 Ligands: ZN.18 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.17 MN.24: 5 residues within 4Å: Chain E: D.203, K.210, D.280, E.282 Ligands: ZN.23 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.21 MN.29: 5 residues within 4Å: Chain F: D.203, K.210, D.280, E.282 Ligands: ZN.28 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.24

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

CL.3: 5 residues within 4Å: Chain A: W.21, G.22, E.23, K.24, A.25 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain A: S.413, A.414 Chain E: N.361 Ligand excluded by PLIP CL.5: 5 residues within 4Å: Chain A: A.281, E.282, G.283, R.284, L.308 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain A: W.78, A.83, R.88 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain B: G.22, E.23, K.24 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain B: A.281, G.283, R.284, L.308 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain B: S.413, A.414 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain B: W.78, A.83, R.88 Ligand excluded by PLIP CL.15: 4 residues within 4Å: Chain C: A.281, G.283, R.284, L.308 Ligand excluded by PLIP CL.16: 2 residues within 4Å: Chain C: S.413, A.414 Ligand excluded by PLIP CL.17: 3 residues within 4Å: Chain C: W.78, A.83, R.88 Ligand excluded by PLIP CL.20: 4 residues within 4Å: Chain D: A.281, G.283, R.284, L.308 Ligand excluded by PLIP CL.21: 2 residues within 4Å: Chain D: S.413, A.414 Ligand excluded by PLIP CL.22: 2 residues within 4Å: Chain D: L.44, R.73 Ligand excluded by PLIP CL.25: 5 residues within 4Å: Chain E: A.281, E.282, G.283, R.284, L.308 Ligand excluded by PLIP CL.26: 3 residues within 4Å: Chain E: P.84, S.413, A.414 Ligand excluded by PLIP CL.27: 3 residues within 4Å: Chain E: W.78, A.83, R.88 Ligand excluded by PLIP CL.30: 4 residues within 4Å: Chain F: A.281, G.283, R.284, L.308 Ligand excluded by PLIP CL.31: 3 residues within 4Å: Chain F: P.84, S.413, A.414 Ligand excluded by PLIP CL.32: 3 residues within 4Å: Chain F: W.78, A.83, R.88 Ligand excluded by PLIP CL.33: 3 residues within 4Å: Chain F: G.239, L.240, N.241 Ligand excluded by PLIP

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

2019-05-15

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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