SMTL ID : 4bht.1

Structural Determinants of Cofactor Specificity and Domain Flexibility in Bacterial Glutamate Dehydrogenases

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-hexamer

Ligands

18 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 6 residues within 4Å: Chain A: E.8, L.11, N.12, Q.15, A.25, R.29 Ligand excluded by PLIP GOL.2: 7 residues within 4Å: Chain A: G.202, Q.386, N.387, R.390, L.391, G.392 Chain D: P.123 Ligand excluded by PLIP GOL.3: 7 residues within 4Å: Chain A: Y.155, R.156 Chain B: L.186, S.187, N.188 Ligands: GOL.4, GOL.5 Ligand excluded by PLIP GOL.4: 10 residues within 4Å: Chain A: R.156, H.157 Chain B: N.188 Chain C: R.156, H.157 Chain E: N.188 Ligands: GOL.3, GOL.5, GOL.6, GOL.7 Ligand excluded by PLIP GOL.5: 10 residues within 4Å: Chain B: S.187, N.188, N.189 Chain C: R.156, H.157, L.158, G.159, T.162 Ligands: GOL.3, GOL.4 Ligand excluded by PLIP GOL.6: 10 residues within 4Å: Chain A: R.156, H.157, L.158, G.159, T.162 Chain E: S.187, N.188, N.189 Ligands: GOL.4, GOL.7 Ligand excluded by PLIP GOL.7: 8 residues within 4Å: Chain A: H.157 Chain C: Y.155, R.156 Chain E: L.186, S.187, N.188 Ligands: GOL.4, GOL.6 Ligand excluded by PLIP GOL.8: 8 residues within 4Å: Chain C: G.202, G.203, Q.386, N.387, R.390, L.391, G.392 Chain F: P.123 Ligand excluded by PLIP GOL.9: 10 residues within 4Å: Chain A: M.48 Chain C: V.68, N.72, I.74 Chain E: E.140, G.141, M.144, R.145 Ligands: EPE.11, GOL.17 Ligand excluded by PLIP GOL.10: 6 residues within 4Å: Chain C: L.11, N.12, Q.15, A.25, Q.26, R.29 Ligand excluded by PLIP GOL.12: 7 residues within 4Å: Chain D: E.8, L.11, N.12, Q.15, A.25, Q.26, R.29 Ligand excluded by PLIP GOL.13: 6 residues within 4Å: Chain A: N.188 Chain B: R.156, H.157 Chain D: R.156, H.157 Chain F: N.188 Ligand excluded by PLIP GOL.14: 11 residues within 4Å: Chain D: G.202, G.203, Q.386, N.387, R.390, L.391, G.392 Chain E: T.121, L.122, P.123, K.436 Ligand excluded by PLIP GOL.15: 8 residues within 4Å: Chain C: N.188 Chain D: N.188 Chain E: R.156, H.157 Chain F: R.156, H.157 Ligands: GOL.16, GOL.19 Ligand excluded by PLIP GOL.16: 11 residues within 4Å: Chain D: S.187, N.188, N.189 Chain E: R.156, H.157, L.158, G.159, T.162 Chain F: R.156 Ligands: GOL.15, GOL.19 Ligand excluded by PLIP GOL.17: 4 residues within 4Å: Chain C: N.72 Chain E: D.70, S.139 Ligands: GOL.9 Ligand excluded by PLIP GOL.19: 7 residues within 4Å: Chain D: L.186, S.187, N.188 Chain F: Y.155, R.156 Ligands: GOL.15, GOL.16 Ligand excluded by PLIP GOL.20: 3 residues within 4Å: Chain F: W.36, E.40, R.46 Ligand excluded by PLIP

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.11: 14 residues within 4Å: Chain C: V.68, D.69, D.70, N.72, R.145 Chain E: V.68, D.69, D.70, R.71, N.72, G.141, M.144, R.145 Ligands: GOL.9 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain E Hydrogen bonds: C:D.70, E:R.145 Salt bridges: C:D.70

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.18: 18 residues within 4Å: Chain A: S.86, A.87, I.88, G.89, T.121, P.123, Q.444 Chain E: K.184, T.190, K.197, F.201, G.202, G.203, Q.386, N.387, R.390, L.391, G.392 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:K.184, E:N.387, A:T.121 Water bridges: E:R.390

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sharkey, M.A. et al., Structure of Nadp(+) -Dependent Glutamate Dehydrogenase from Escherichia Coli: Reflections on the Basis of Coenzyme Specificity in the Family of Glutamate Dehydrogenases. FEBS J. (2013)

Release Date

2013-06-19

Peptides

NADP-SPECIFIC GLUTAMATE DEHYDROGENASE: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

NADP-SPECIFIC GLUTAMATE DEHYDROGENASE

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