SMTL ID : 5lhk.1

Bottromycin maturation enzyme BotP in complex with Mn

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.32 Å

Oligo State

homo-hexamer

Ligands

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

MN.1: 6 residues within 4Å: Chain A: K.261, D.266, D.284, E.345 Ligands: MN.2, BCT.3 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.266, A:D.284, A:E.345, H2O.2, H2O.7 MN.2: 4 residues within 4Å: Chain A: D.266, D.343, E.345 Ligands: MN.1 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.266, A:D.343, A:E.345, H2O.2, H2O.10 MN.4: 6 residues within 4Å: Chain B: K.261, D.266, D.284, E.345 Ligands: MN.5, BCT.6 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.266, B:D.284, B:E.345, H2O.14, H2O.20 MN.5: 4 residues within 4Å: Chain B: D.266, D.343, E.345 Ligands: MN.4 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.266, B:D.343, B:E.345, H2O.14, H2O.22 MN.7: 6 residues within 4Å: Chain C: K.261, D.266, D.284, E.345 Ligands: MN.8, BCT.9 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.266, C:D.284, C:E.345, H2O.27, H2O.32 MN.8: 4 residues within 4Å: Chain C: D.266, D.343, E.345 Ligands: MN.7 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.266, C:D.343, C:E.345, H2O.27, H2O.35 MN.10: 6 residues within 4Å: Chain D: K.261, D.266, D.284, E.345 Ligands: MN.11, BCT.12 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.266, D:D.284, D:E.345, H2O.40, H2O.45 MN.11: 4 residues within 4Å: Chain D: D.266, D.343, E.345 Ligands: MN.10 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.266, D:D.343, D:E.345, H2O.40, H2O.48 MN.13: 6 residues within 4Å: Chain E: K.261, D.266, D.284, E.345 Ligands: MN.14, BCT.15 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.266, E:D.284, E:E.345, H2O.53, H2O.58 MN.14: 4 residues within 4Å: Chain E: D.266, D.343, E.345 Ligands: MN.13 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.266, E:D.343, E:E.345, H2O.53, H2O.60 MN.16: 6 residues within 4Å: Chain F: K.261, D.266, D.284, E.345 Ligands: MN.17, BCT.18 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:D.266, F:D.284, F:E.345, H2O.65, H2O.70 MN.17: 4 residues within 4Å: Chain F: D.266, D.343, E.345 Ligands: MN.16 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:D.266, F:D.343, F:E.345, H2O.65, H2O.73

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

BCT.3: 8 residues within 4Å: Chain A: K.261, D.343, N.344, E.345, G.346, R.347, L.374 Ligands: MN.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.347, A:R.347, A:L.374 BCT.6: 8 residues within 4Å: Chain B: K.261, D.343, N.344, E.345, G.346, R.347, L.374 Ligands: MN.4 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.347, B:R.347, B:L.374 BCT.9: 8 residues within 4Å: Chain C: K.261, D.343, N.344, E.345, G.346, R.347, L.374 Ligands: MN.7 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.347, C:R.347, C:L.374 BCT.12: 8 residues within 4Å: Chain D: K.261, D.343, N.344, E.345, G.346, R.347, L.374 Ligands: MN.10 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.347, D:R.347, D:L.374 BCT.15: 8 residues within 4Å: Chain E: K.261, D.343, N.344, E.345, G.346, R.347, L.374 Ligands: MN.13 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:R.347, E:R.347, E:L.374 BCT.18: 8 residues within 4Å: Chain F: K.261, D.343, N.344, E.345, G.346, R.347, L.374 Ligands: MN.16 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:R.347, F:R.347, F:L.374

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mann, G. et al., Structure and Substrate Recognition of the Bottromycin Maturation Enzyme BotP. Chembiochem (2016)

Release Date

2016-10-05

Peptides

Leucine aminopeptidase 2, chloroplastic: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

Leucine aminopeptidase 2, chloroplastic

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