SMTL ID : 7lox.1

The structure of Agmatinase from E. Coli at 3.2 A displaying guanidine in the active site

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

homo-hexamer

Ligands

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

MN.1: 6 residues within 4Å: Chain A: D.149, H.151, D.230, D.232 Ligands: MN.2, GAI.3 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.149, A:H.151, A:D.230, A:D.232, A:D.232 MN.2: 6 residues within 4Å: Chain A: H.126, D.149, D.153, D.230 Ligands: MN.1, GAI.3 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:H.126, A:D.149, A:D.149, A:D.153, A:D.230 MN.5: 6 residues within 4Å: Chain B: D.149, H.151, D.230, D.232 Ligands: MN.6, GAI.7 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.149, B:H.151, B:D.230, B:D.232, B:D.232 MN.6: 6 residues within 4Å: Chain B: H.126, D.149, D.153, D.230 Ligands: MN.5, GAI.7 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.126, B:D.149, B:D.153, B:D.230 MN.8: 7 residues within 4Å: Chain C: D.149, A.150, H.151, D.230, D.232 Ligands: MN.9, GAI.10 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.149, C:H.151, C:D.230, C:D.232, C:D.232 MN.9: 6 residues within 4Å: Chain C: H.126, D.149, D.153, D.230 Ligands: MN.8, GAI.10 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.126, C:D.149, C:D.153, C:D.230 MN.11: 6 residues within 4Å: Chain D: D.149, H.151, D.230, D.232 Ligands: MN.12, GAI.13 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.149, D:H.151, D:D.230, D:D.232, D:D.232 MN.12: 6 residues within 4Å: Chain D: H.126, D.149, D.153, D.230 Ligands: MN.11, GAI.13 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:H.126, D:D.149, D:D.149, D:D.153, D:D.230 MN.15: 6 residues within 4Å: Chain E: D.149, H.151, D.230, D.232 Ligands: MN.16, GAI.17 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:D.149, E:H.151, E:D.230, E:D.232, E:D.232 MN.16: 6 residues within 4Å: Chain E: H.126, D.149, D.153, D.230 Ligands: MN.15, GAI.17 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:H.126, E:D.149, E:D.153, E:D.230 MN.18: 7 residues within 4Å: Chain F: D.149, A.150, H.151, D.230, D.232 Ligands: MN.19, GAI.20 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:D.149, F:H.151, F:D.230, F:D.232, F:D.232 MN.19: 6 residues within 4Å: Chain F: H.126, D.149, D.153, D.230 Ligands: MN.18, GAI.20 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:H.126, F:D.149, F:D.153, F:D.230

8 x GAI: GUANIDINE(Non-covalent)

GAI.3: 11 residues within 4Å: Chain A: H.126, D.149, H.151, D.153, H.163, D.230, D.232, T.244, E.274 Ligands: MN.1, MN.2 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.244, A:T.244 Salt bridges: A:D.149, A:D.153, A:D.230, A:D.232, A:E.274 GAI.4: 7 residues within 4Å: Chain A: H.151, T.152, D.153, T.154, T.188, E.189 Chain C: W.68 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:T.152, A:T.152, A:T.152, A:T.152, A:D.153, A:T.154, A:T.188 Salt bridges: A:D.153 GAI.7: 10 residues within 4Å: Chain B: H.126, D.149, H.151, D.153, H.163, D.230, D.232, T.244 Ligands: MN.5, MN.6 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:H.163, B:T.244, B:T.244, B:T.244 Salt bridges: B:D.149, B:D.153, B:D.230, B:D.232, B:E.274 GAI.10: 11 residues within 4Å: Chain C: H.126, D.149, H.151, D.153, H.163, D.230, D.232, T.244, E.274 Ligands: MN.8, MN.9 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:H.151, C:H.163, C:H.163 Salt bridges: C:D.149, C:D.153, C:D.230, C:D.232, C:E.274 GAI.13: 11 residues within 4Å: Chain D: H.126, D.149, H.151, D.153, H.163, D.230, D.232, T.244, E.274 Ligands: MN.11, MN.12 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:H.163, D:T.244 Salt bridges: D:D.149, D:D.153, D:D.230, D:D.232, D:E.274 GAI.14: 7 residues within 4Å: Chain D: H.151, T.152, D.153, T.154, T.188, E.189 Chain F: W.68 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:T.152, D:T.152, D:T.152, D:D.153, D:T.154, D:T.188 Salt bridges: D:D.153 GAI.17: 10 residues within 4Å: Chain E: H.126, D.149, H.151, D.153, H.163, D.230, D.232, T.244 Ligands: MN.15, MN.16 8 PLIP interactions: 8 interactions with chain E Hydrogen bonds: E:H.163, E:T.244, E:T.244 Salt bridges: E:D.149, E:D.153, E:D.230, E:D.232, E:E.274 GAI.20: 11 residues within 4Å: Chain F: H.126, D.149, H.151, D.153, H.163, D.230, D.232, T.244, E.274 Ligands: MN.18, MN.19 8 PLIP interactions: 8 interactions with chain F Hydrogen bonds: F:H.163, F:H.163, F:T.244 Salt bridges: F:D.149, F:D.153, F:D.230, F:D.232, F:E.274

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Maturana, P. et al., Crystal Structure of Escherichia coli Agmatinase: Catalytic Mechanism and Residues Relevant for Substrate Specificity. Int J Mol Sci (2021)

Release Date

2021-05-12

Peptides

Agmatinase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

Agmatinase

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