SMTL ID : 5cev.1 (1 other biounit)

ARGINASE FROM BACILLUS CALDEVELOX, L-LYSINE COMPLEX

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-hexamer

Ligands

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

MN.1: 5 residues within 4Å: Chain A: H.99, D.122, D.126, D.226 Ligands: MN.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.99, A:D.122, A:D.126, A:D.226, H2O.1 MN.2: 5 residues within 4Å: Chain A: D.122, H.124, D.226, D.228 Ligands: MN.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.122, A:H.124, A:D.226, A:D.228, H2O.1 MN.5: 5 residues within 4Å: Chain B: H.99, D.122, D.126, D.226 Ligands: MN.6 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.99, B:D.122, B:D.126, B:D.226, H2O.1 MN.6: 5 residues within 4Å: Chain B: D.122, H.124, D.226, D.228 Ligands: MN.5 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.122, B:H.124, B:D.226, B:D.228, H2O.1 MN.10: 5 residues within 4Å: Chain C: H.99, D.122, D.126, D.226 Ligands: MN.11 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.99, C:D.122, C:D.126, C:D.226, H2O.1 MN.11: 5 residues within 4Å: Chain C: D.122, H.124, D.226, D.228 Ligands: MN.10 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.122, C:H.124, C:D.226, C:D.228, H2O.1 MN.13: 5 residues within 4Å: Chain D: H.99, D.122, D.126, D.226 Ligands: MN.14 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.99, D:D.122, D:D.126, D:D.226, H2O.8 MN.14: 5 residues within 4Å: Chain D: D.122, H.124, D.226, D.228 Ligands: MN.13 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.122, D:H.124, D:D.226, D:D.228, H2O.8 MN.17: 5 residues within 4Å: Chain E: H.99, D.122, D.126, D.226 Ligands: MN.18 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:H.99, E:D.122, E:D.126, E:D.226, H2O.8 MN.18: 5 residues within 4Å: Chain E: D.122, H.124, D.226, D.228 Ligands: MN.17 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.122, E:H.124, E:D.226, E:D.228, H2O.8 MN.22: 5 residues within 4Å: Chain F: H.99, D.122, D.126, D.226 Ligands: MN.23 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:H.99, F:D.122, F:D.126, F:D.226, H2O.8 MN.23: 5 residues within 4Å: Chain F: D.122, H.124, D.226, D.228 Ligands: MN.22 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.122, F:H.124, F:D.226, F:D.228, H2O.8

6 x LYS: LYSINE(Non-covalent)

LYS.3: 9 residues within 4Å: Chain A: D.126, N.128, S.135, H.139, G.140, D.178, E.181, T.240, E.271 10 PLIP interactions: 8 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: A:N.128, A:S.135, A:D.178, A:T.240, A:E.271, K.3, K.3 Water bridges: A:G.140, A:G.140, A:D.178 LYS.4: 9 residues within 4Å: Chain B: D.126, N.128, S.135, H.139, G.140, D.178, E.181, T.240, E.271 11 PLIP interactions: 9 interactions with chain B, 2 Ligand-Ligand interactions Hydrogen bonds: B:N.128, B:S.135, B:D.178, B:T.240, B:E.271, K.4, K.4 Water bridges: B:D.126, B:N.137, B:H.139, B:G.140 LYS.9: 10 residues within 4Å: Chain C: H.124, D.126, N.128, S.135, H.139, G.140, D.178, E.181, T.240, E.271 10 PLIP interactions: 8 interactions with chain C, 2 Ligand-Ligand interactions Hydrogen bonds: C:N.128, C:S.135, C:D.178, C:E.271, K.9, K.9 Water bridges: C:D.126, C:N.137, C:G.140, C:G.140 LYS.15: 9 residues within 4Å: Chain D: D.126, N.128, S.135, H.139, G.140, D.178, E.181, T.240, E.271 10 PLIP interactions: 8 interactions with chain D, 2 Ligand-Ligand interactions Hydrogen bonds: D:N.128, D:S.135, D:D.178, D:E.271, K.15, K.15 Water bridges: D:H.139, D:G.140, D:G.140, D:D.178 LYS.16: 9 residues within 4Å: Chain E: D.126, N.128, S.135, H.139, G.140, D.178, E.181, T.240, E.271 9 PLIP interactions: 7 interactions with chain E, 2 Ligand-Ligand interactions Hydrogen bonds: E:N.128, E:S.135, E:D.178, E:E.271, K.16, K.16 Water bridges: E:D.126, E:N.137, E:G.140 LYS.21: 10 residues within 4Å: Chain F: H.124, D.126, N.128, S.135, H.139, G.140, D.178, E.181, T.240, E.271 11 PLIP interactions: 9 interactions with chain F, 2 Ligand-Ligand interactions Hydrogen bonds: F:N.128, F:S.135, F:D.178, F:T.240, F:E.271, K.21, K.21 Water bridges: F:D.126, F:N.137, F:G.140, F:G.140

6 x GAI: GUANIDINE(Non-covalent)

GAI.7: 8 residues within 4Å: Chain A: R.249, H.252, L.253, E.256, L.298 Chain B: M.195, H.196, D.199 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:M.195 Salt bridges: B:D.199, A:E.256 GAI.8: 7 residues within 4Å: Chain B: H.252, L.253, E.256, L.298 Chain C: M.195, H.196, D.199 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:M.195 Salt bridges: C:D.199, B:E.256 GAI.12: 7 residues within 4Å: Chain A: M.195, H.196, D.199 Chain C: H.252, L.253, E.256, L.298 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:M.195 Salt bridges: A:D.199, C:E.256 GAI.19: 8 residues within 4Å: Chain D: R.249, H.252, L.253, E.256, L.298 Chain E: M.195, H.196, D.199 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain E Salt bridges: D:E.256, E:D.199 Hydrogen bonds: E:M.195 GAI.20: 7 residues within 4Å: Chain E: H.252, L.253, E.256, L.298 Chain F: M.195, H.196, D.199 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:M.195 Salt bridges: F:D.199, E:E.256 GAI.24: 7 residues within 4Å: Chain D: M.195, H.196, D.199 Chain F: H.252, L.253, E.256, L.298 3 PLIP interactions: 1 interactions with chain F, 2 interactions with chain D Salt bridges: F:E.256, D:D.199 Hydrogen bonds: D:M.195

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bewley, M.C. et al., Crystal structures of Bacillus caldovelox arginase in complex with substrate and inhibitors reveal new insights into activation, inhibition and catalysis in the arginase superfamily. Structure Fold.Des. (1999)

Release Date

1999-04-16

Peptides

PROTEIN (ARGINASE): ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

PROTEIN (ARGINASE)

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