SMTL ID : 4xgi.1

Crystal structure of Glutamate dehydrogenase from Burkholderia thailandensis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-hexamer

Ligands

6 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.1: 22 residues within 4Å: Chain A: R.94, D.166, V.167, N.168, R.206, T.210, Q.237, G.238, F.239, G.240, N.241, V.242, D.262, H.263, A.313, A.314, L.315, G.335, A.336, N.337, N.362 Ligands: AKG.2 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:T.210, A:V.242, A:N.362 Hydrogen bonds: A:R.94, A:D.166, A:N.168, A:R.206, A:R.206, A:T.210, A:T.210, A:Q.237, A:F.239, A:G.240, A:N.241, A:V.242, A:H.263, A:H.263, A:A.314, A:N.337, A:N.337 Water bridges: A:T.210, A:G.243, A:D.262, A:L.315, A:Q.318 pi-Cation interactions: A:K.126, A:H.263 NAD.4: 23 residues within 4Å: Chain B: R.94, K.114, D.166, V.167, N.168, R.206, T.210, Q.237, G.238, F.239, G.240, N.241, V.242, D.262, H.263, A.313, A.314, L.315, G.335, A.336, N.337, N.362 Ligands: AKG.5 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: B:T.210, B:V.242, B:N.362 Hydrogen bonds: B:R.94, B:D.166, B:N.168, B:R.206, B:R.206, B:T.210, B:Q.237, B:F.239, B:G.240, B:N.241, B:V.242, B:H.263, B:H.263, B:A.314, B:N.337, B:N.337 Water bridges: B:T.210, B:G.243, B:L.315 pi-Cation interactions: B:K.126, B:H.263 NAD.7: 23 residues within 4Å: Chain C: R.94, D.166, V.167, N.168, R.206, T.210, Q.237, G.238, F.239, G.240, N.241, V.242, Q.261, D.262, H.263, A.313, A.314, L.315, G.335, A.336, N.337, N.362 Ligands: AKG.8 23 PLIP interactions: 23 interactions with chain C Hydrophobic interactions: C:T.210, C:V.242 Hydrogen bonds: C:R.94, C:D.166, C:N.168, C:R.206, C:R.206, C:T.210, C:Q.237, C:F.239, C:G.240, C:N.241, C:V.242, C:H.263, C:H.263, C:A.314, C:N.337, C:N.337 Water bridges: C:T.210, C:G.243, C:L.315, C:Q.318 pi-Cation interactions: C:K.126 NAD.10: 22 residues within 4Å: Chain D: R.94, D.166, V.167, N.168, R.206, T.210, Q.237, G.238, F.239, G.240, N.241, V.242, D.262, H.263, A.313, A.314, L.315, G.335, A.336, N.337, N.362 Ligands: AKG.11 30 PLIP interactions: 30 interactions with chain D Hydrophobic interactions: D:T.210, D:V.242, D:N.362 Hydrogen bonds: D:R.94, D:D.166, D:N.168, D:R.206, D:R.206, D:T.210, D:T.210, D:Q.237, D:F.239, D:G.240, D:N.241, D:V.242, D:H.263, D:H.263, D:A.314, D:N.337, D:N.337 Water bridges: D:R.94, D:D.262, D:D.262, D:G.286, D:L.315, D:Q.318, D:Q.318, D:Q.318 pi-Cation interactions: D:K.126, D:H.263 NAD.13: 23 residues within 4Å: Chain E: R.94, K.114, D.166, V.167, N.168, R.206, T.210, Q.237, G.238, F.239, G.240, N.241, V.242, D.262, H.263, A.313, A.314, L.315, G.335, A.336, N.337, N.362 Ligands: AKG.14 28 PLIP interactions: 28 interactions with chain E Hydrophobic interactions: E:T.210, E:V.242, E:N.362 Hydrogen bonds: E:R.94, E:D.166, E:N.168, E:R.206, E:R.206, E:T.210, E:Q.237, E:F.239, E:N.241, E:N.241, E:V.242, E:H.263, E:H.263, E:A.314, E:N.337, E:N.337 Water bridges: E:T.210, E:G.240, E:G.240, E:D.262, E:L.315, E:L.315, E:Q.318 pi-Cation interactions: E:K.126, E:H.263 NAD.16: 23 residues within 4Å: Chain F: R.94, K.114, D.166, V.167, N.168, R.206, T.210, Q.237, G.238, F.239, G.240, N.241, V.242, D.262, H.263, A.313, A.314, L.315, G.335, A.336, N.337, N.362 Ligands: AKG.17 27 PLIP interactions: 27 interactions with chain F Hydrophobic interactions: F:T.210, F:V.242, F:N.362 Hydrogen bonds: F:R.94, F:D.166, F:N.168, F:R.206, F:R.206, F:T.210, F:T.210, F:F.239, F:N.241, F:V.242, F:H.263, F:H.263, F:A.314, F:N.337, F:N.337 Water bridges: F:T.210, F:Q.237, F:Q.237, F:G.240, F:G.243, F:D.262, F:D.262 pi-Cation interactions: F:K.126, F:H.263

6 x AKG: 2-OXOGLUTARIC ACID(Non-covalent)

AKG.2: 16 residues within 4Å: Chain A: K.90, G.91, G.92, M.111, K.114, K.126, A.164, P.165, D.166, T.194, R.206, N.337, G.365, V.366, S.369 Ligands: NAD.1 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:V.366 Hydrogen bonds: A:G.92, A:D.166, A:T.194, A:N.337, A:G.365, A:S.369 Water bridges: A:K.126 Salt bridges: A:K.90, A:K.114, A:K.126, A:R.206 AKG.5: 15 residues within 4Å: Chain B: K.90, G.91, G.92, M.111, K.114, K.126, A.164, P.165, D.166, R.206, N.337, G.365, V.366, S.369 Ligands: NAD.4 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:V.366 Hydrogen bonds: B:G.92, B:D.166, B:T.194, B:N.337, B:S.369 Water bridges: B:K.114 Salt bridges: B:K.90, B:K.114, B:K.126, B:R.206 AKG.8: 16 residues within 4Å: Chain C: K.90, G.91, G.92, M.111, K.114, K.126, A.164, P.165, D.166, T.194, R.206, N.337, G.365, V.366, S.369 Ligands: NAD.7 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:A.164 Hydrogen bonds: C:G.92, C:D.166, C:T.194, C:N.337, C:S.369 Water bridges: C:K.126 Salt bridges: C:K.90, C:K.114, C:K.126, C:R.206 AKG.11: 16 residues within 4Å: Chain D: K.90, G.91, G.92, M.111, K.114, K.126, A.164, P.165, D.166, T.194, R.206, N.337, G.365, V.366, S.369 Ligands: NAD.10 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:A.164 Hydrogen bonds: D:G.92, D:D.166, D:T.194, D:N.337, D:G.365, D:S.369 Water bridges: D:K.114 Salt bridges: D:K.90, D:K.114, D:K.126, D:R.206 AKG.14: 16 residues within 4Å: Chain E: K.90, G.91, G.92, M.111, K.114, K.126, A.164, P.165, D.166, T.194, R.206, N.337, G.365, V.366, S.369 Ligands: NAD.13 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:G.92, E:D.166, E:N.337, E:S.369 Water bridges: E:K.114 Salt bridges: E:K.90, E:K.114, E:K.126, E:R.206 AKG.17: 16 residues within 4Å: Chain F: K.90, G.91, G.92, M.111, K.114, K.126, A.164, P.165, D.166, T.194, R.206, N.337, G.365, V.366, S.369 Ligands: NAD.16 12 PLIP interactions: 12 interactions with chain F Hydrophobic interactions: F:V.366 Hydrogen bonds: F:G.91, F:G.92, F:D.166, F:T.194, F:N.337, F:S.369 Water bridges: F:K.126 Salt bridges: F:K.90, F:K.114, F:K.126, F:R.206

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

EDO.3: 3 residues within 4Å: Chain A: A.406, E.407, V.411 No protein-ligand interaction detected (PLIP) EDO.6: 5 residues within 4Å: Chain B: L.354, W.403, A.406, V.411, V.413 No protein-ligand interaction detected (PLIP) EDO.9: 4 residues within 4Å: Chain C: W.403, A.406, E.407, V.411 No protein-ligand interaction detected (PLIP) EDO.12: 4 residues within 4Å: Chain D: A.406, E.407, V.411, V.413 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:A.406 Water bridges: D:V.413 EDO.15: 2 residues within 4Å: Chain E: W.403, V.411 No protein-ligand interaction detected (PLIP) EDO.18: 3 residues within 4Å: Chain F: W.403, A.406, V.411 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Abendroth, J. et al., Crystal structure of Glutamate dehydrogenase from Burkholderia thailandensis. to be published

Release Date

2015-01-14

Peptides

Glutamate dehydrogenase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Glutamate dehydrogenase