SMTL ID : 6jv0.1

Crystal Structure of N-terminal domain of ArgZ, bound to Product, an arginine dihydrolase from the Ornithine-Ammonia Cycle in Cyanobacteria

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.14 Å

Oligo State

monomer

Ligands

1 x ORN: L-ornithine(Non-covalent)

ORN.1: 13 residues within 4Å: Chain A: I.42, N.43, M.46, D.86, F.89, N.92, R.111, R.160, Y.188, H.189, A.279, G.280, C.285 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.89 Hydrogen bonds: A:N.43, A:D.86, A:N.92 Salt bridges: A:R.111, A:R.160, A:H.189

17 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 8 residues within 4Å: Chain A: D.147, R.148, W.154, P.196, L.197, G.200, Y.201, I.221 Ligand excluded by PLIP EDO.3: 4 residues within 4Å: Chain A: E.60, Q.61, K.64, P.272 Ligand excluded by PLIP EDO.4: 5 residues within 4Å: Chain A: R.148, N.243, V.244, N.245, R.289 Ligand excluded by PLIP EDO.5: 8 residues within 4Å: Chain A: I.42, N.43, P.44, H.108, F.159, R.160, E.185, Y.188 Ligand excluded by PLIP EDO.6: 1 residues within 4Å: Chain A: I.74 Ligand excluded by PLIP EDO.7: 4 residues within 4Å: Chain A: H.166, P.167, A.170, K.171 Ligand excluded by PLIP EDO.8: 3 residues within 4Å: Chain A: P.44, W.45, R.186 Ligand excluded by PLIP EDO.9: 4 residues within 4Å: Chain A: W.45, N.49, L.277, K.278 Ligand excluded by PLIP EDO.10: 6 residues within 4Å: Chain A: L.232, D.233, N.236, L.252, V.253, S.254 Ligand excluded by PLIP EDO.11: 8 residues within 4Å: Chain A: S.198, G.199, Y.201, N.245, D.246, A.264, G.265, F.266 Ligand excluded by PLIP EDO.12: 7 residues within 4Å: Chain A: L.97, F.146, D.147, R.148, G.150, E.292, P.293 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain A: V.177, V.178, S.179, Y.212 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain A: L.77, V.78, K.79, P.80 Ligand excluded by PLIP EDO.15: 1 residues within 4Å: Chain A: Y.157 Ligand excluded by PLIP EDO.16: 5 residues within 4Å: Chain A: F.106, Y.107, Q.112, Q.134, D.135 Ligand excluded by PLIP EDO.17: 1 residues within 4Å: Chain A: L.232 Ligand excluded by PLIP EDO.18: 6 residues within 4Å: Chain A: I.28, A.241, V.242, N.243, K.284, R.289 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhuang, N. et al., Crystal structures and biochemical analyses of the bacterial arginine dihydrolase ArgZ suggests a "bond rotation" catalytic mechanism. J.Biol.Chem. (2020)

Release Date

2020-01-15

Peptides

Sll1336 protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Sll1336 protein