SMTL ID : 4o6r.1

Crystal Structure of a Putative Aldehyde Dehydrogenase from Burkholderia cenocepacia

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-tetramer

Ligands

4 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.1: 16 residues within 4Å: Chain A: I.153, V.154, P.155, K.180, S.182, E.183, G.213, G.217, Q.218, F.231, T.232, G.233, S.234, T.237, R.240, I.241 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:V.154, A:V.154, A:K.180, A:E.183, A:Q.218, A:S.234, A:S.234, A:T.237, A:R.240 Water bridges: A:G.213 AMP.6: 15 residues within 4Å: Chain B: I.153, V.154, K.180, S.182, E.183, G.213, G.217, Q.218, F.231, T.232, G.233, S.234, T.237, R.240, I.241 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:V.154, B:K.180, B:E.183, B:G.213, B:Q.218, B:S.234, B:S.234, B:T.237 Water bridges: B:S.234 AMP.11: 12 residues within 4Å: Chain C: I.153, V.154, K.180, S.182, E.183, G.213, G.217, Q.218, F.231, G.233, S.234, T.237 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:K.180, C:E.183, C:G.213, C:Q.218, C:S.234, C:S.234 Water bridges: C:H.214, C:T.237 AMP.19: 14 residues within 4Å: Chain D: I.153, V.154, P.155, K.180, S.182, E.183, G.213, G.217, Q.218, F.231, T.232, G.233, S.234, T.237 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:K.180, D:Q.218, D:S.234, D:S.234 Water bridges: D:G.213, D:T.237

8 x NO3: NITRATE ION(Non-functional Binders)

NO3.2: 6 residues within 4Å: Chain A: R.112, F.158, H.283, A.288, I.290, K.448 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.112, A:R.112, A:H.283 NO3.5: 8 residues within 4Å: Chain A: V.134, D.135, F.138, W.483 Chain C: R.449, V.450, N.451 Ligands: EDO.16 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain C Hydrogen bonds: A:D.135, C:R.449, C:R.449, C:V.450, C:N.451 NO3.7: 6 residues within 4Å: Chain B: R.112, F.158, H.283, A.288, I.290, K.448 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.112, B:R.112, B:H.283 NO3.9: 8 residues within 4Å: Chain B: V.134, D.135, F.138, W.483 Chain D: R.449, V.450, N.451 Ligands: EDO.24 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:R.449, D:R.449, D:V.450, D:N.451, B:D.135 NO3.10: 7 residues within 4Å: Chain A: R.449, V.450, N.451 Chain C: V.134, D.135, F.138, W.483 5 PLIP interactions: 1 interactions with chain C, 4 interactions with chain A Hydrogen bonds: C:D.135, A:R.449, A:R.449, A:V.450, A:N.451 NO3.12: 6 residues within 4Å: Chain C: R.112, F.158, H.283, A.288, I.290, K.448 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.112, C:R.112 NO3.18: 7 residues within 4Å: Chain B: R.449, V.450, N.451 Chain D: V.134, D.135, F.138, W.483 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:R.449, B:R.449, B:V.450, B:N.451, D:D.135 NO3.20: 6 residues within 4Å: Chain D: R.112, F.158, H.283, A.288, I.290, K.448 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.112, D:R.112

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

EDO.3: 1 residues within 4Å: Chain A: F.138 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D Water bridges: B:R.432, B:A.435, D:Q.143 EDO.13: 5 residues within 4Å: Chain C: A.379, K.380, L.399, R.400, I.410 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.400 EDO.14: 5 residues within 4Å: Chain C: A.382, T.383, A.409, I.410, A.413 No protein-ligand interaction detected (PLIP) EDO.15: 2 residues within 4Å: Chain C: F.138, L.139 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B Water bridges: D:R.432, B:Q.143 EDO.16: 6 residues within 4Å: Chain C: R.112, W.279, K.448, R.449, V.450 Ligands: NO3.5 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:V.450, C:V.450 Water bridges: C:R.112, C:W.279, C:R.449 EDO.21: 5 residues within 4Å: Chain D: A.379, K.380, L.399, R.400, I.410 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.400 Water bridges: D:E.378 EDO.22: 3 residues within 4Å: Chain D: A.382, T.383, A.413 1 PLIP interactions: 1 interactions with chain D Water bridges: D:I.410 EDO.23: 1 residues within 4Å: Chain D: L.139 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.143 EDO.24: 6 residues within 4Å: Chain D: R.112, W.279, K.448, R.449, V.450 Ligands: NO3.9 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.112, D:V.450, D:V.450

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: D.271, N.275, R.308, L.312 Chain C: R.496 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.271, A:N.275, A:R.308, A:R.308 GOL.8: 5 residues within 4Å: Chain B: D.271, N.275, R.308, L.312 Chain D: R.496 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:D.271, B:N.275, B:R.308 Water bridges: D:R.496, D:R.496 GOL.17: 5 residues within 4Å: Chain A: R.496 Chain C: D.271, N.275, R.308, L.312 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:D.271, C:N.275, C:R.308 Water bridges: A:R.496 GOL.25: 4 residues within 4Å: Chain B: R.496 Chain D: D.271, N.275, R.308 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:N.275, D:N.275, D:R.308, D:R.308 Water bridges: B:R.496

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dranow, D.M. et al., Crystal Structure of a Putative Aldehyde Dehydrogenase from Burkholderia cenocepacia. TO BE PUBLISHED

Release Date

2014-01-22

Peptides

Aldehyde Dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Aldehyde Dehydrogenase