SMTL ID : 6wsa.1

Crystal structure of a betaine aldehyde dehydrogenase from Burkholderia pseudomallei without cofactor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-tetramer

Ligands

4 x SIN: SUCCINIC ACID(Non-covalent)

SIN.1: 3 residues within 4Å: Chain A: S.2, G.5, L.6 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.6 Hydrogen bonds: A:S.2 SIN.16: 3 residues within 4Å: Chain B: S.2, G.5, L.6 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.6 Hydrogen bonds: B:S.2 SIN.31: 3 residues within 4Å: Chain C: S.2, G.5, L.6 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.6 Water bridges: C:S.2 SIN.46: 3 residues within 4Å: Chain D: S.2, G.5, L.6 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:L.6 Water bridges: D:S.2

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

EDO.2: 7 residues within 4Å: Chain A: R.140, E.470, H.471, T.473, I.475 Chain D: T.467, H.471 Ligand excluded by PLIP EDO.3: 4 residues within 4Å: Chain A: Y.154, Q.157, W.161, V.284 Ligand excluded by PLIP EDO.4: 3 residues within 4Å: Chain A: R.82, E.190, E.194 Ligand excluded by PLIP EDO.5: 8 residues within 4Å: Chain A: I.149, K.176, G.209, G.212, A.213, F.226, T.232, V.236 Ligand excluded by PLIP EDO.6: 4 residues within 4Å: Chain A: T.275, F.279, G.444 Chain D: V.488 Ligand excluded by PLIP EDO.7: 3 residues within 4Å: Chain A: R.58, E.59, A.62 Ligand excluded by PLIP EDO.8: 2 residues within 4Å: Chain A: S.2, L.34 Ligand excluded by PLIP EDO.9: 5 residues within 4Å: Chain A: L.79, R.80, N.83, I.106, V.107 Ligand excluded by PLIP EDO.10: 4 residues within 4Å: Chain A: D.47, V.50, A.51, H.218 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain A: D.262, Q.294, Q.295, A.296, E.398 Ligand excluded by PLIP EDO.12: 5 residues within 4Å: Chain A: D.267, R.304, A.307, R.308, R.311 Ligand excluded by PLIP EDO.13: 3 residues within 4Å: Chain A: L.337, D.341, G.354 Ligand excluded by PLIP EDO.14: 5 residues within 4Å: Chain A: P.219, G.220, A.222, R.474 Chain D: K.456 Ligand excluded by PLIP EDO.17: 7 residues within 4Å: Chain B: R.140, E.470, H.471, T.473, I.475 Chain C: T.467, H.471 Ligand excluded by PLIP EDO.18: 4 residues within 4Å: Chain B: Y.154, Q.157, W.161, V.284 Ligand excluded by PLIP EDO.19: 3 residues within 4Å: Chain B: R.82, E.190, E.194 Ligand excluded by PLIP EDO.20: 8 residues within 4Å: Chain B: I.149, K.176, G.209, G.212, A.213, F.226, T.232, V.236 Ligand excluded by PLIP EDO.21: 4 residues within 4Å: Chain B: T.275, F.279, G.444 Chain C: V.488 Ligand excluded by PLIP EDO.22: 3 residues within 4Å: Chain B: R.58, E.59, A.62 Ligand excluded by PLIP EDO.23: 2 residues within 4Å: Chain B: S.2, L.34 Ligand excluded by PLIP EDO.24: 5 residues within 4Å: Chain B: L.79, R.80, N.83, I.106, V.107 Ligand excluded by PLIP EDO.25: 4 residues within 4Å: Chain B: D.47, V.50, A.51, H.218 Ligand excluded by PLIP EDO.26: 5 residues within 4Å: Chain B: D.262, Q.294, Q.295, A.296, E.398 Ligand excluded by PLIP EDO.27: 5 residues within 4Å: Chain B: D.267, R.304, A.307, R.308, R.311 Ligand excluded by PLIP EDO.28: 3 residues within 4Å: Chain B: L.337, D.341, G.354 Ligand excluded by PLIP EDO.29: 5 residues within 4Å: Chain B: P.219, G.220, A.222, R.474 Chain C: K.456 Ligand excluded by PLIP EDO.32: 7 residues within 4Å: Chain B: T.467, H.471 Chain C: R.140, E.470, H.471, T.473, I.475 Ligand excluded by PLIP EDO.33: 4 residues within 4Å: Chain C: Y.154, Q.157, W.161, V.284 Ligand excluded by PLIP EDO.34: 3 residues within 4Å: Chain C: R.82, E.190, E.194 Ligand excluded by PLIP EDO.35: 8 residues within 4Å: Chain C: I.149, K.176, G.209, G.212, A.213, F.226, T.232, V.236 Ligand excluded by PLIP EDO.36: 4 residues within 4Å: Chain B: V.488 Chain C: T.275, F.279, G.444 Ligand excluded by PLIP EDO.37: 3 residues within 4Å: Chain C: R.58, E.59, A.62 Ligand excluded by PLIP EDO.38: 2 residues within 4Å: Chain C: S.2, L.34 Ligand excluded by PLIP EDO.39: 5 residues within 4Å: Chain C: L.79, R.80, N.83, I.106, V.107 Ligand excluded by PLIP EDO.40: 4 residues within 4Å: Chain C: D.47, V.50, A.51, H.218 Ligand excluded by PLIP EDO.41: 5 residues within 4Å: Chain C: D.262, Q.294, Q.295, A.296, E.398 Ligand excluded by PLIP EDO.42: 5 residues within 4Å: Chain C: D.267, R.304, A.307, R.308, R.311 Ligand excluded by PLIP EDO.43: 3 residues within 4Å: Chain C: L.337, D.341, G.354 Ligand excluded by PLIP EDO.44: 5 residues within 4Å: Chain B: K.456 Chain C: P.219, G.220, A.222, R.474 Ligand excluded by PLIP EDO.47: 7 residues within 4Å: Chain A: T.467, H.471 Chain D: R.140, E.470, H.471, T.473, I.475 Ligand excluded by PLIP EDO.48: 4 residues within 4Å: Chain D: Y.154, Q.157, W.161, V.284 Ligand excluded by PLIP EDO.49: 3 residues within 4Å: Chain D: R.82, E.190, E.194 Ligand excluded by PLIP EDO.50: 8 residues within 4Å: Chain D: I.149, K.176, G.209, G.212, A.213, F.226, T.232, V.236 Ligand excluded by PLIP EDO.51: 4 residues within 4Å: Chain A: V.488 Chain D: T.275, F.279, G.444 Ligand excluded by PLIP EDO.52: 3 residues within 4Å: Chain D: R.58, E.59, A.62 Ligand excluded by PLIP EDO.53: 2 residues within 4Å: Chain D: S.2, L.34 Ligand excluded by PLIP EDO.54: 5 residues within 4Å: Chain D: L.79, R.80, N.83, I.106, V.107 Ligand excluded by PLIP EDO.55: 4 residues within 4Å: Chain D: D.47, V.50, A.51, H.218 Ligand excluded by PLIP EDO.56: 5 residues within 4Å: Chain D: D.262, Q.294, Q.295, A.296, E.398 Ligand excluded by PLIP EDO.57: 5 residues within 4Å: Chain D: D.267, R.304, A.307, R.308, R.311 Ligand excluded by PLIP EDO.58: 3 residues within 4Å: Chain D: L.337, D.341, G.354 Ligand excluded by PLIP EDO.59: 5 residues within 4Å: Chain A: K.456 Chain D: P.219, G.220, A.222, R.474 Ligand excluded by PLIP

4 x NA: SODIUM ION(Non-functional Binders)

NA.15: 4 residues within 4Å: Chain A: T.26, F.27, D.93, V.180 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.26, A:F.27, A:D.93, A:D.93 NA.30: 4 residues within 4Å: Chain B: T.26, F.27, D.93, V.180 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.26, B:F.27, B:D.93, B:D.93 NA.45: 4 residues within 4Å: Chain C: T.26, F.27, D.93, V.180 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:F.27, C:V.180 NA.60: 4 residues within 4Å: Chain D: T.26, F.27, D.93, V.180 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:F.27, D:D.93

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Beard, D.K. et al., Crystal structure of betaine aldehyde dehydrogenase from Burkholderia pseudomallei. Acta Crystallogr.,Sect.F (2022)

Release Date

2020-05-20

Peptides

NAD/NADP-dependent betaine aldehyde dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

NAD/NADP-dependent betaine aldehyde dehydrogenase

Related Entries With Identical Sequence