SMTL ID : 4cev.1 (1 other biounit)

ARGINASE FROM BACILLUS CALDEVELOX, L-ORNITHINE COMPLEX

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-octamer

Ligands

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

MN.1: 6 residues within 4Å: Chain A: H.99, D.122, D.126, D.226 Ligands: MN.2, ORN.3 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.10: 6 residues within 4Å: Chain B: H.99, D.122, D.126, D.226 Ligands: ORN.4, MN.11 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.11: 5 residues within 4Å: Chain B: D.122, H.124, D.226, D.228 Ligands: MN.10 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.13: 6 residues within 4Å: Chain C: H.99, D.122, D.126, D.226 Ligands: ORN.5, MN.14 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.14: 5 residues within 4Å: Chain C: D.122, H.124, D.226, D.228 Ligands: MN.13 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.16: 6 residues within 4Å: Chain D: H.99, D.122, D.126, D.226 Ligands: ORN.6, MN.17 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.1 MN.17: 5 residues within 4Å: Chain D: D.122, H.124, D.226, D.228 Ligands: MN.16 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.1 MN.19: 6 residues within 4Å: Chain E: H.99, D.122, D.126, D.226 Ligands: MN.20, ORN.21 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.5 MN.20: 5 residues within 4Å: Chain E: D.122, H.124, D.226, D.228 Ligands: MN.19 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.5 MN.28: 6 residues within 4Å: Chain F: H.99, D.122, D.126, D.226 Ligands: ORN.22, MN.29 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.5 MN.29: 5 residues within 4Å: Chain F: D.122, H.124, D.226, D.228 Ligands: MN.28 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.5 MN.31: 6 residues within 4Å: Chain G: H.99, D.122, D.126, D.226 Ligands: ORN.23, MN.32 5 PLIP interactions: 4 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:H.99, G:D.122, G:D.126, G:D.226, H2O.5 MN.32: 5 residues within 4Å: Chain G: D.122, H.124, D.226, D.228 Ligands: MN.31 5 PLIP interactions: 4 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:D.122, G:H.124, G:D.226, G:D.228, H2O.5 MN.34: 6 residues within 4Å: Chain H: H.99, D.122, D.126, D.226 Ligands: ORN.24, MN.35 5 PLIP interactions: 4 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:H.99, H:D.122, H:D.126, H:D.226, H2O.5 MN.35: 5 residues within 4Å: Chain H: D.122, H.124, D.226, D.228 Ligands: MN.34 5 PLIP interactions: 4 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:D.122, H:H.124, H:D.226, H:D.228, H2O.5

12 x ORN: L-ornithine(Non-covalent)(Non-functional Binders)

ORN.3: 11 residues within 4Å: Chain A: H.124, D.126, N.128, P.134, S.135, H.139, G.140, D.178, E.181, T.240 Ligands: MN.1 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:N.128, A:S.135, A:H.139, A:E.181 Water bridges: A:D.126, A:D.126, A:S.135, A:N.137, A:G.140, A:G.140 ORN.4: 10 residues within 4Å: Chain B: H.124, D.126, N.128, S.135, H.139, G.140, D.178, E.181, T.240 Ligands: MN.10 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:N.128, B:S.135, B:H.139 Water bridges: B:D.126, B:D.126, B:N.137, B:N.137, B:G.140, B:S.176, B:E.181 ORN.5: 11 residues within 4Å: Chain C: H.124, D.126, N.128, P.134, S.135, H.139, G.140, D.178, E.181, T.240 Ligands: MN.13 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:N.128, C:S.135, C:H.139 Water bridges: C:D.126, C:D.126, C:S.135, C:N.137, C:G.140, C:G.140, C:S.176, C:E.181 ORN.6: 11 residues within 4Å: Chain D: H.124, D.126, N.128, P.134, S.135, H.139, G.140, D.178, E.181, T.240 Ligands: MN.16 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:N.128, D:S.135, D:H.139 Water bridges: D:D.126, D:S.135, D:N.137, D:N.137, D:S.176, D:E.181, D:E.181 ORN.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) ORN.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) ORN.21: 11 residues within 4Å: Chain E: H.124, D.126, N.128, P.134, S.135, H.139, G.140, D.178, E.181, T.240 Ligands: MN.19 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:N.128, E:S.135, E:H.139, E:E.181 Water bridges: E:D.126, E:D.126, E:S.135, E:N.137, E:G.140, E:G.140 ORN.22: 10 residues within 4Å: Chain F: H.124, D.126, N.128, S.135, H.139, G.140, D.178, E.181, T.240 Ligands: MN.28 10 PLIP interactions: 10 interactions with chain F Hydrogen bonds: F:N.128, F:S.135, F:H.139 Water bridges: F:D.126, F:D.126, F:N.137, F:N.137, F:G.140, F:S.176, F:E.181 ORN.23: 11 residues within 4Å: Chain G: H.124, D.126, N.128, P.134, S.135, H.139, G.140, D.178, E.181, T.240 Ligands: MN.31 11 PLIP interactions: 11 interactions with chain G Hydrogen bonds: G:N.128, G:S.135, G:H.139 Water bridges: G:D.126, G:D.126, G:S.135, G:N.137, G:G.140, G:G.140, G:S.176, G:E.181 ORN.24: 11 residues within 4Å: Chain H: H.124, D.126, N.128, P.134, S.135, H.139, G.140, D.178, E.181, T.240 Ligands: MN.34 10 PLIP interactions: 10 interactions with chain H Hydrogen bonds: H:N.128, H:S.135, H:H.139 Water bridges: H:D.126, H:S.135, H:N.137, H:N.137, H:S.176, H:E.181, H:E.181 ORN.25: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) ORN.26: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

8 x GAI: GUANIDINE(Non-covalent)

GAI.9: 7 residues within 4Å: Chain A: R.249, H.252, E.256, L.298 Chain B: M.195, H.196, D.199 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Salt bridges: A:E.256, B:D.199 Hydrogen bonds: B:M.195 GAI.12: 7 residues within 4Å: Chain B: R.249, H.252, L.253, E.256 Chain C: M.195, H.196, D.199 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:M.195, B:R.249 Salt bridges: C:D.199, B:E.256 GAI.15: 8 residues within 4Å: Chain A: M.195, H.196, D.199 Chain C: R.249, H.252, L.253, E.256, L.298 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A Salt bridges: C:E.256, A:D.199 Hydrogen bonds: A:M.195 GAI.18: 5 residues within 4Å: Chain D: R.249, H.252, L.253, E.256, L.298 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.249 Salt bridges: D:E.256 GAI.27: 7 residues within 4Å: Chain E: R.249, H.252, 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.30: 7 residues within 4Å: Chain F: R.249, H.252, L.253, E.256 Chain G: M.195, H.196, D.199 4 PLIP interactions: 2 interactions with chain F, 2 interactions with chain G Hydrogen bonds: F:R.249, G:M.195 Salt bridges: F:E.256, G:D.199 GAI.33: 8 residues within 4Å: Chain E: M.195, H.196, D.199 Chain G: R.249, H.252, L.253, E.256, L.298 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain G Hydrogen bonds: E:M.195 Salt bridges: E:D.199, G:E.256 GAI.36: 5 residues within 4Å: Chain H: R.249, H.252, L.253, E.256, L.298 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:R.249 Salt bridges: H:E.256

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): ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
A

F
B

G
C

H
D

PROTEIN (ARGINASE)

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