SMTL ID : 6azs.1 (2 other biounits)

Structural and biochemical characterization of a non-canonical biuret hydrolase (BiuH) from the cyanuric acid catabolism pathway of Rhizobium leguminasorum bv. viciae 3841

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.59 Å

Oligo State

homo-tetramer

Ligands

4 x BTB: 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

BTB.1: 11 residues within 4Å: Chain A: N.178, R.181, I.182, E.183, R.206, G.207, Y.208 Chain B: N.178, Q.179, R.181 Ligands: BTB.4 8 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B, 1 interactions with chain D Hydrogen bonds: A:R.181, A:R.206, B:Q.179, B:Q.179, B:R.181 Water bridges: A:E.183, B:N.178, D:A.115 BTB.4: 11 residues within 4Å: Chain A: N.178, Q.179, R.181 Chain B: N.178, R.181, I.182, E.183, R.206, G.207, Y.208 Ligands: BTB.1 8 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A, 1 interactions with chain C Hydrogen bonds: B:R.181, B:R.206, A:Q.179, A:Q.179 Water bridges: B:E.183, A:N.178, A:R.181, C:A.115 BTB.6: 11 residues within 4Å: Chain C: N.178, R.181, I.182, E.183, R.206, G.207, Y.208 Chain D: N.178, Q.179, R.181 Ligands: BTB.8 7 PLIP interactions: 3 interactions with chain C, 3 interactions with chain D, 1 interactions with chain B Hydrogen bonds: C:R.181, C:R.206, D:Q.179, D:Q.179 Water bridges: C:E.183, D:N.178, B:A.115 BTB.8: 11 residues within 4Å: Chain C: N.178, Q.179, R.181 Chain D: N.178, R.181, I.182, E.183, R.206, G.207, Y.208 Ligands: BTB.6 8 PLIP interactions: 4 interactions with chain D, 3 interactions with chain C, 1 interactions with chain A Hydrogen bonds: D:R.181, D:R.206, C:Q.179, C:Q.179 Water bridges: D:E.183, D:E.183, C:N.178, A:A.115

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: E.174, R.206 Chain B: E.174, N.178 Chain D: A.170 10 PLIP interactions: 6 interactions with chain A, 3 interactions with chain B, 1 interactions with chain D Hydrogen bonds: A:E.174, B:N.178, D:A.170 Water bridges: A:E.174, A:E.174, A:R.206, A:R.206, A:R.206, B:E.174, B:E.174 GOL.7: 6 residues within 4Å: Chain B: A.170 Chain C: E.174, R.206 Chain D: E.174, N.178 Ligands: GOL.11 7 PLIP interactions: 1 interactions with chain D, 5 interactions with chain C, 1 interactions with chain B Hydrogen bonds: D:N.178, C:E.174, B:A.170 Water bridges: C:E.174, C:E.174, C:R.206, C:R.206 GOL.11: 7 residues within 4Å: Chain A: A.170 Chain C: E.174, L.175, N.178 Chain D: E.174, R.206 Ligands: GOL.7 7 PLIP interactions: 5 interactions with chain D, 1 interactions with chain C, 1 interactions with chain A Water bridges: D:E.174, D:E.174, D:E.174, D:R.206, D:R.206 Hydrogen bonds: C:N.178, A:A.170

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 2 residues within 4Å: Chain A: N.28, R.29 Ligand excluded by PLIP

2 x C5S: N-formyl-D-aspartic acid(Covalent)

C5S.5: 10 residues within 4Å: Chain B: D.56, F.61, V.68, E.104, K.165, I.190, T.191, V.194, C.195 Chain C: Q.235 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:F.61, B:T.191 Hydrogen bonds: B:D.56, B:E.104, B:E.104, B:T.191, B:C.195, C:Q.235 Salt bridges: B:K.165 C5S.9: 8 residues within 4Å: Chain A: Q.235 Chain D: D.56, F.61, E.104, I.190, T.191, V.194, C.195 8 PLIP interactions: 2 interactions with chain A, 6 interactions with chain D Hydrogen bonds: A:Q.235, A:Q.235, D:E.104, D:T.191, D:C.195 Hydrophobic interactions: D:F.61, D:T.191 Salt bridges: D:K.165

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.10: 3 residues within 4Å: Chain D: L.77, A.80, Y.222 1 PLIP interactions: 1 interactions with chain D Water bridges: D:H.225

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Esquirol, L. et al., Structural and biochemical characterization of the biuret hydrolase (BiuH) from the cyanuric acid catabolism pathway of Rhizobium leguminasorum bv. viciae 3841. PLoS ONE (2018)

Release Date

2018-02-21

Peptides

Putative amidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Putative amidase

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