SMTL ID : 6bun.1

Crystal structures of cyanuric acid hydrolase from Moorella thermoacetica

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.78 Å

Oligo State

homo-tetramer

Ligands

4 x MLI: MALONATE ION(Non-functional Binders)

MLI.1: 11 residues within 4Å: Chain A: G.46, R.53, S.84, G.85, K.162, M.190, S.232, A.233, R.324, S.343, G.344 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:G.85, A:S.232, A:A.233, A:G.344 Salt bridges: A:K.41, A:R.53, A:K.162, A:K.295, A:R.324 MLI.10: 10 residues within 4Å: Chain B: G.46, R.53, S.84, G.85, K.162, S.232, A.233, R.324, S.343, G.344 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:G.85, B:S.232, B:A.233, B:G.344 Salt bridges: B:K.41, B:R.53, B:K.162, B:K.295, B:R.324 MLI.13: 7 residues within 4Å: Chain B: T.57, V.76, F.81, E.236, L.237, E.241 Ligands: PDO.15 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.237 Hydrogen bonds: B:E.236 Water bridges: B:E.236, B:E.241 MLI.17: 11 residues within 4Å: Chain C: G.46, R.53, S.84, G.85, K.162, M.190, S.232, A.233, R.324, S.343, G.344 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:G.85, C:G.85, C:A.233, C:G.344 Salt bridges: C:K.41, C:R.53, C:K.162, C:K.295, C:R.324

8 x CA: CALCIUM ION(Non-covalent)

CA.2: 6 residues within 4Å: Chain A: E.297, A.346, Q.349, G.350, P.351, G.354 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:A.346, A:Q.349, A:P.351, A:G.354, H2O.2 CA.9: 4 residues within 4Å: Chain A: A.108, G.110, T.249, S.251 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:A.108, A:G.110, H2O.1, H2O.3, H2O.13 CA.11: 6 residues within 4Å: Chain B: E.297, A.346, Q.349, G.350, P.351, G.354 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.297, B:A.346, B:Q.349, B:P.351, B:G.354 CA.12: 1 residues within 4Å: Chain B: E.169 5 PLIP interactions: 5 Ligand-Water interactions Metal complexes: H2O.7, H2O.25, H2O.26, H2O.27, H2O.38 CA.18: 6 residues within 4Å: Chain C: E.297, A.346, Q.349, G.350, P.351, G.354 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:A.346, C:Q.349, C:P.351, C:G.354, H2O.38 CA.23: 4 residues within 4Å: Chain C: A.108, P.109, G.110, S.251 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:A.108, C:G.110, H2O.30, H2O.32 CA.24: 3 residues within 4Å: Chain B: S.315 Chain C: S.315, N.318 No protein-ligand interaction detected (PLIP) CA.25: 6 residues within 4Å: Chain D: E.297, A.346, Q.349, G.350, P.351, G.354 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.297, D:Q.349, D:P.351, D:G.354, H2O.47

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

CL.3: 5 residues within 4Å: Chain A: I.266, D.267, A.268, D.269, R.305 Ligand excluded by PLIP CL.14: 5 residues within 4Å: Chain B: I.266, D.267, A.268, D.269, R.305 Ligand excluded by PLIP CL.19: 2 residues within 4Å: Chain C: E.132, N.135 Ligand excluded by PLIP CL.26: 4 residues within 4Å: Chain D: E.297, A.298, H.319, T.320 Ligand excluded by PLIP

15 x PDO: 1,3-PROPANDIOL(Non-covalent)

PDO.4: 3 residues within 4Å: Chain A: S.282, D.283, D.284 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:D.283 PDO.5: 2 residues within 4Å: Chain A: R.308, D.313 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Water bridges: A:R.308, A:R.308, C:E.43 PDO.6: 6 residues within 4Å: Chain A: W.222, E.297, A.298, A.346, E.347, D.352 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.222 Water bridges: A:A.346, A:H.348 PDO.7: 3 residues within 4Å: Chain A: G.54, T.57, Q.58 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.57 Hydrogen bonds: A:G.54, A:Q.58 PDO.8: 2 residues within 4Å: Chain A: D.284, D.287 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.287 PDO.15: 7 residues within 4Å: Chain B: D.50, R.53, K.162, G.234, V.235, E.236 Ligands: MLI.13 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:R.53, B:E.236 Hydrogen bonds: B:D.50, B:R.53, B:V.235, B:E.236 Water bridges: B:M.83 PDO.16: 5 residues within 4Å: Chain B: E.6, V.7, F.8, L.255, R.362 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.7, B:R.362 Water bridges: B:V.7 PDO.20: 5 residues within 4Å: Chain C: F.51, R.170, V.235 Chain D: S.14, D.16 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:S.14, C:R.170 Water bridges: C:R.170 PDO.21: 5 residues within 4Å: Chain C: E.6, V.7, F.8, L.255, R.362 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:V.7, C:R.362 Water bridges: C:V.7 PDO.22: 9 residues within 4Å: Chain A: E.88, I.317, R.321, A.325 Chain C: E.88, I.317, R.321, S.322, A.325 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:A.325 PDO.27: 5 residues within 4Å: Chain D: E.207, I.208, N.223, L.224, Y.225 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.223, D:Y.225 PDO.28: 4 residues within 4Å: Chain D: V.48, D.50, F.51, R.53 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:F.51 Hydrogen bonds: D:V.48, D:R.53 PDO.29: 5 residues within 4Å: Chain D: E.6, V.7, F.8, L.255, R.362 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:V.7, D:R.362 Water bridges: D:V.7 PDO.30: 7 residues within 4Å: Chain B: E.88, G.89, R.321, A.325 Chain D: I.317, S.322, A.325 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain D Hydrophobic interactions: B:E.88, B:A.325 Hydrogen bonds: B:G.89, D:S.322 Water bridges: D:G.89, D:S.322 PDO.31: 5 residues within 4Å: Chain D: G.46, C.47, R.53, G.344, G.345 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:C.47, D:R.53 Water bridges: D:R.194

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shi, K. et al., Crystal structures of Moorella thermoacetica cyanuric acid hydrolase reveal conformational flexibility and asymmetry important for catalysis. Plos One (2019)

Release Date

2019-06-12

Peptides

Cyanuric acid amidohydrolase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Cyanuric acid amidohydrolase

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