SMTL ID : 1hwy.1

BOVINE GLUTAMATE DEHYDROGENASE COMPLEXED WITH NAD AND 2-OXOGLUTARATE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

homo-hexamer

Ligands

24 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 4 residues within 4Å: Chain A: H.209, G.210 Ligands: PO4.2, PO4.4 Ligand excluded by PLIP PO4.2: 7 residues within 4Å: Chain A: S.213, R.261, Y.262, R.265, H.450 Ligands: PO4.1, PO4.4 Ligand excluded by PLIP PO4.3: 2 residues within 4Å: Chain A: R.217, H.450 Ligand excluded by PLIP PO4.4: 3 residues within 4Å: Chain A: K.446 Ligands: PO4.1, PO4.2 Ligand excluded by PLIP PO4.8: 7 residues within 4Å: Chain B: S.213, R.261, Y.262, R.265, H.450 Ligands: PO4.9, PO4.10 Ligand excluded by PLIP PO4.9: 4 residues within 4Å: Chain B: H.209, G.210 Ligands: PO4.8, PO4.10 Ligand excluded by PLIP PO4.10: 3 residues within 4Å: Chain B: K.446 Ligands: PO4.8, PO4.9 Ligand excluded by PLIP PO4.11: 2 residues within 4Å: Chain B: R.217, H.450 Ligand excluded by PLIP PO4.15: 7 residues within 4Å: Chain C: S.213, R.261, Y.262, R.265, H.450 Ligands: PO4.16, PO4.17 Ligand excluded by PLIP PO4.16: 4 residues within 4Å: Chain C: H.209, G.210 Ligands: PO4.15, PO4.17 Ligand excluded by PLIP PO4.17: 3 residues within 4Å: Chain C: K.446 Ligands: PO4.15, PO4.16 Ligand excluded by PLIP PO4.18: 2 residues within 4Å: Chain C: R.217, H.450 Ligand excluded by PLIP PO4.22: 7 residues within 4Å: Chain D: S.213, R.261, Y.262, R.265, H.450 Ligands: PO4.23, PO4.25 Ligand excluded by PLIP PO4.23: 4 residues within 4Å: Chain D: H.209, G.210 Ligands: PO4.22, PO4.25 Ligand excluded by PLIP PO4.24: 2 residues within 4Å: Chain D: R.217, H.450 Ligand excluded by PLIP PO4.25: 3 residues within 4Å: Chain D: K.446 Ligands: PO4.22, PO4.23 Ligand excluded by PLIP PO4.29: 7 residues within 4Å: Chain E: S.213, R.261, Y.262, R.265, H.450 Ligands: PO4.30, PO4.32 Ligand excluded by PLIP PO4.30: 4 residues within 4Å: Chain E: H.209, G.210 Ligands: PO4.29, PO4.32 Ligand excluded by PLIP PO4.31: 2 residues within 4Å: Chain E: R.217, H.450 Ligand excluded by PLIP PO4.32: 3 residues within 4Å: Chain E: K.446 Ligands: PO4.29, PO4.30 Ligand excluded by PLIP PO4.36: 2 residues within 4Å: Chain F: R.217, H.450 Ligand excluded by PLIP PO4.37: 7 residues within 4Å: Chain F: S.213, R.261, Y.262, R.265, H.450 Ligands: PO4.38, PO4.39 Ligand excluded by PLIP PO4.38: 4 residues within 4Å: Chain F: H.209, G.210 Ligands: PO4.37, PO4.39 Ligand excluded by PLIP PO4.39: 3 residues within 4Å: Chain F: K.446 Ligands: PO4.37, PO4.38 Ligand excluded by PLIP

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

AKG.5: 15 residues within 4Å: Chain A: K.90, G.92, M.111, K.114, K.126, A.166, P.167, N.168, T.199, R.211, N.349, N.374, V.378, S.381 Ligands: NAD.7 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:A.166, A:V.378 Hydrogen bonds: A:G.92, A:N.168, A:T.199, A:N.349, A:S.381 Salt bridges: A:K.90, A:K.114, A:K.126, A:R.211 AKG.12: 15 residues within 4Å: Chain B: K.90, G.92, M.111, K.114, K.126, A.166, P.167, N.168, T.199, R.211, N.349, N.374, V.378, S.381 Ligands: NAD.14 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:A.166, B:V.378 Hydrogen bonds: B:G.92, B:N.168, B:T.199, B:N.349, B:S.381 Salt bridges: B:K.90, B:K.114, B:K.126, B:R.211 AKG.19: 15 residues within 4Å: Chain C: K.90, G.92, M.111, K.114, K.126, A.166, P.167, N.168, T.199, R.211, N.349, N.374, V.378, S.381 Ligands: NAD.21 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:A.166, C:V.378 Hydrogen bonds: C:G.92, C:N.168, C:T.199, C:N.349, C:S.381 Salt bridges: C:K.90, C:K.114, C:K.126, C:R.211 AKG.26: 15 residues within 4Å: Chain D: K.90, G.92, M.111, K.114, K.126, A.166, P.167, N.168, T.199, R.211, N.349, N.374, V.378, S.381 Ligands: NAD.28 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:A.166, D:V.378 Hydrogen bonds: D:G.92, D:N.168, D:T.199, D:N.349, D:S.381 Salt bridges: D:K.90, D:K.114, D:K.126, D:R.211 AKG.33: 15 residues within 4Å: Chain E: K.90, G.92, M.111, K.114, K.126, A.166, P.167, N.168, T.199, R.211, N.349, N.374, V.378, S.381 Ligands: NAD.35 11 PLIP interactions: 11 interactions with chain E Hydrophobic interactions: E:A.166, E:V.378 Hydrogen bonds: E:G.92, E:N.168, E:T.199, E:N.349, E:S.381 Salt bridges: E:K.90, E:K.114, E:K.126, E:R.211 AKG.40: 15 residues within 4Å: Chain F: K.90, G.92, M.111, K.114, K.126, A.166, P.167, N.168, T.199, R.211, N.349, N.374, V.378, S.381 Ligands: NAD.41 11 PLIP interactions: 11 interactions with chain F Hydrophobic interactions: F:A.166, F:V.378 Hydrogen bonds: F:G.92, F:N.168, F:T.199, F:N.349, F:S.381 Salt bridges: F:K.90, F:K.114, F:K.126, F:R.211

12 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Covalent)(Non-covalent)

NAD.6: 21 residues within 4Å: Chain A: H.195, Q.205, G.206, K.387, N.388, N.390, H.391, V.392, S.393, E.445 Chain B: Q.85, R.86, T.87, C.115, A.116, D.119, V.120, P.121, F.122, Y.382, K.488 15 PLIP interactions: 10 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:R.86, B:T.87, B:T.87, B:D.119, B:V.120, B:V.120, B:F.122, B:K.488, A:N.388, A:S.393, A:S.393 pi-Cation interactions: B:R.86, B:R.86 Salt bridges: A:K.387, A:K.387 NAD.7: 25 residues within 4Å: Chain A: R.94, N.168, M.169, S.170, R.211, T.215, Q.250, G.251, F.252, G.253, N.254, V.255, G.274, E.275, S.276, K.295, A.325, A.326, S.327, Q.330, G.347, A.348, N.349, N.374 Ligands: AKG.5 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:T.215, A:N.374 Hydrogen bonds: A:R.94, A:N.168, A:S.170, A:R.211, A:Q.250, A:G.251, A:F.252, A:F.252, A:N.254, A:N.254, A:V.255, A:E.275, A:S.276, A:K.295, A:A.326, A:S.327, A:S.327, A:Q.330, A:N.349, A:N.349 NAD.13: 21 residues within 4Å: Chain B: H.195, Q.205, G.206, K.387, N.388, N.390, H.391, V.392, S.393, E.445 Chain F: Q.85, R.86, T.87, C.115, A.116, D.119, V.120, P.121, F.122, Y.382, K.488 15 PLIP interactions: 10 interactions with chain F, 5 interactions with chain B Hydrogen bonds: F:R.86, F:T.87, F:T.87, F:D.119, F:V.120, F:V.120, F:F.122, F:K.488, B:N.388, B:S.393, B:S.393 pi-Cation interactions: F:R.86, F:R.86 Salt bridges: B:K.387, B:K.387 NAD.14: 25 residues within 4Å: Chain B: R.94, N.168, M.169, S.170, R.211, T.215, Q.250, G.251, F.252, G.253, N.254, V.255, G.274, E.275, S.276, K.295, A.325, A.326, S.327, Q.330, G.347, A.348, N.349, N.374 Ligands: AKG.12 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:T.215, B:N.374 Hydrogen bonds: B:R.94, B:N.168, B:S.170, B:R.211, B:Q.250, B:G.251, B:F.252, B:F.252, B:N.254, B:N.254, B:V.255, B:E.275, B:S.276, B:K.295, B:A.326, B:S.327, B:S.327, B:Q.330, B:N.349, B:N.349 NAD.20: 21 residues within 4Å: Chain C: H.195, Q.205, G.206, K.387, N.388, N.390, H.391, V.392, S.393, E.445 Chain E: Q.85, R.86, T.87, C.115, A.116, D.119, V.120, P.121, F.122, Y.382, K.488 17 PLIP interactions: 5 interactions with chain C, 12 interactions with chain E Hydrogen bonds: C:N.388, C:S.393, C:S.393, E:R.86, E:T.87, E:T.87, E:D.119, E:D.119, E:V.120, E:V.120, E:F.122, E:Y.382, E:K.488 Salt bridges: C:K.387, C:K.387 pi-Cation interactions: E:R.86, E:R.86 NAD.21: 25 residues within 4Å: Chain C: R.94, N.168, M.169, S.170, R.211, T.215, Q.250, G.251, F.252, G.253, N.254, V.255, G.274, E.275, S.276, K.295, A.325, A.326, S.327, Q.330, G.347, A.348, N.349, N.374 Ligands: AKG.19 23 PLIP interactions: 23 interactions with chain C Hydrophobic interactions: C:T.215, C:N.374 Hydrogen bonds: C:R.94, C:N.168, C:S.170, C:R.211, C:T.215, C:Q.250, C:G.251, C:F.252, C:F.252, C:N.254, C:N.254, C:V.255, C:E.275, C:S.276, C:K.295, C:A.326, C:S.327, C:S.327, C:Q.330, C:N.349, C:N.349 NAD.27: 21 residues within 4Å: Chain C: Q.85, R.86, T.87, C.115, A.116, D.119, V.120, P.121, F.122, Y.382, K.488 Chain D: H.195, Q.205, G.206, K.387, N.388, N.390, H.391, V.392, S.393, E.445 16 PLIP interactions: 5 interactions with chain D, 11 interactions with chain C Hydrogen bonds: D:N.388, D:S.393, D:S.393, C:R.86, C:T.87, C:T.87, C:D.119, C:V.120, C:V.120, C:F.122, C:Y.382, C:K.488 Salt bridges: D:K.387, D:K.387 pi-Cation interactions: C:R.86, C:R.86 NAD.28: 25 residues within 4Å: Chain D: R.94, N.168, M.169, S.170, R.211, T.215, Q.250, G.251, F.252, G.253, N.254, V.255, G.274, E.275, S.276, K.295, A.325, A.326, S.327, Q.330, G.347, A.348, N.349, N.374 Ligands: AKG.26 22 PLIP interactions: 22 interactions with chain D Hydrophobic interactions: D:T.215, D:N.374 Hydrogen bonds: D:R.94, D:N.168, D:S.170, D:R.211, D:Q.250, D:G.251, D:F.252, D:F.252, D:N.254, D:N.254, D:V.255, D:E.275, D:S.276, D:K.295, D:A.326, D:S.327, D:S.327, D:Q.330, D:N.349, D:N.349 NAD.34: 21 residues within 4Å: Chain D: Q.85, R.86, T.87, C.115, A.116, D.119, V.120, P.121, F.122, Y.382, K.488 Chain E: H.195, Q.205, G.206, K.387, N.388, N.390, H.391, V.392, S.393, E.445 17 PLIP interactions: 12 interactions with chain D, 5 interactions with chain E Hydrogen bonds: D:R.86, D:T.87, D:T.87, D:D.119, D:D.119, D:V.120, D:V.120, D:F.122, D:Y.382, D:K.488, E:N.388, E:S.393, E:S.393 pi-Cation interactions: D:R.86, D:R.86 Salt bridges: E:K.387, E:K.387 NAD.35: 25 residues within 4Å: Chain E: R.94, N.168, M.169, S.170, R.211, T.215, Q.250, G.251, F.252, G.253, N.254, V.255, G.274, E.275, S.276, K.295, A.325, A.326, S.327, Q.330, G.347, A.348, N.349, N.374 Ligands: AKG.33 22 PLIP interactions: 22 interactions with chain E Hydrophobic interactions: E:T.215, E:N.374 Hydrogen bonds: E:R.94, E:N.168, E:S.170, E:R.211, E:T.215, E:Q.250, E:G.251, E:F.252, E:F.252, E:N.254, E:N.254, E:V.255, E:S.276, E:K.295, E:A.326, E:S.327, E:S.327, E:Q.330, E:N.349, E:N.349 NAD.41: 25 residues within 4Å: Chain F: R.94, N.168, M.169, S.170, R.211, T.215, Q.250, G.251, F.252, G.253, N.254, V.255, G.274, E.275, S.276, K.295, A.325, A.326, S.327, Q.330, G.347, A.348, N.349, N.374 Ligands: AKG.40 22 PLIP interactions: 22 interactions with chain F Hydrophobic interactions: F:T.215, F:N.374 Hydrogen bonds: F:R.94, F:N.168, F:S.170, F:R.211, F:T.215, F:Q.250, F:G.251, F:F.252, F:F.252, F:N.254, F:N.254, F:V.255, F:S.276, F:K.295, F:A.326, F:S.327, F:S.327, F:Q.330, F:N.349, F:N.349 NAD.42: 21 residues within 4Å: Chain A: Q.85, R.86, T.87, C.115, A.116, D.119, V.120, P.121, F.122, Y.382, K.488 Chain F: H.195, Q.205, G.206, K.387, N.388, N.390, H.391, V.392, S.393, E.445 16 PLIP interactions: 11 interactions with chain A, 5 interactions with chain F Hydrogen bonds: A:R.86, A:T.87, A:T.87, A:D.119, A:D.119, A:V.120, A:V.120, A:F.122, A:K.488, F:N.388, F:S.393, F:S.393 pi-Cation interactions: A:R.86, A:R.86 Salt bridges: F:K.387, F:K.387

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Smith, T.J. et al., Structures of bovine glutamate dehydrogenase complexes elucidate the mechanism of purine regulation. J.Mol.Biol. (2001)

Release Date

2001-01-31

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