SMTL ID : 7lba.1 (2 other biounits)

E. coli Agmatinase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-hexamer

Ligands

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

MN.1: 5 residues within 4Å: Chain A: D.172, H.174, D.253, D.255 Ligands: MN.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.172, A:H.174, A:D.253, A:D.255, H2O.4 MN.2: 5 residues within 4Å: Chain A: H.149, D.172, D.176, D.253 Ligands: MN.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.149, A:D.172, A:D.176, A:D.253, H2O.4 MN.3: 5 residues within 4Å: Chain B: D.172, H.174, D.253, D.255 Ligands: MN.4 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.172, B:H.174, B:D.253, B:D.255, H2O.7 MN.4: 5 residues within 4Å: Chain B: H.149, D.172, D.176, D.253 Ligands: MN.3 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.149, B:D.172, B:D.176, B:D.253, H2O.5 MN.5: 5 residues within 4Å: Chain C: D.172, H.174, D.253, D.255 Ligands: MN.6 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.172, C:H.174, C:D.253, C:D.255, C:D.255 MN.6: 5 residues within 4Å: Chain C: H.149, D.172, D.176, D.253 Ligands: MN.5 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.149, C:D.172, C:D.176, C:D.253, H2O.12 MN.7: 5 residues within 4Å: Chain D: D.172, H.174, D.253, D.255 Ligands: MN.8 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.172, D:H.174, D:D.253, D:D.255, D:D.255 MN.8: 6 residues within 4Å: Chain D: H.149, D.172, D.176, H.186, D.253 Ligands: MN.7 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.176, D:D.253, H2O.14 MN.9: 5 residues within 4Å: Chain E: D.172, H.174, D.253, D.255 Ligands: MN.10 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.172, E:H.174, E:D.253, E:D.255, H2O.20 MN.10: 5 residues within 4Å: Chain E: H.149, D.172, D.176, D.253 Ligands: MN.9 6 PLIP interactions: 4 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:H.149, E:D.172, E:D.176, E:D.253, H2O.19, H2O.20 MN.11: 5 residues within 4Å: Chain F: D.172, H.174, D.253, D.255 Ligands: MN.12 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.172, F:H.174, F:D.253, F:D.255, H2O.23 MN.12: 5 residues within 4Å: Chain F: H.149, D.172, D.176, D.253 Ligands: MN.11 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:H.149, F:D.172, F:D.176, F:D.253, H2O.22

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chitrakar, I. et al., Structure of the E. coli agmatinase, SPEB. Plos One (2021)

Release Date

2021-03-31

Peptides

Agmatinase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Agmatinase

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