SMTL ID : 8z2c.1

Crystal structure of apo Aspergillus terreus glutamate dehydrogenase (AtGDH) with open and partially closed conformations (form I)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-hexamer

Ligands

12 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 5 residues within 4Å: Chain A: G.79, G.80, Q.99, K.114, D.154 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.80, A:Q.99 Water bridges: A:Q.99 Salt bridges: A:K.114 ACT.2: 4 residues within 4Å: Chain A: D.252, S.253, K.279, Q.284 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.253, A:Q.284 Salt bridges: A:K.279 ACT.3: 2 residues within 4Å: Chain B: V.60, V.62 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:V.62 Water bridges: B:V.62 ACT.4: 2 residues within 4Å: Chain B: E.206, H.207 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:H.207 ACT.5: 5 residues within 4Å: Chain C: G.79, G.80, Q.99, K.114, D.154 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:G.80, C:Q.99 Water bridges: C:Q.99 Salt bridges: C:K.114 ACT.6: 4 residues within 4Å: Chain C: D.252, S.253, K.279, Q.284 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.253, C:Q.284 Salt bridges: C:K.279 ACT.7: 2 residues within 4Å: Chain D: V.60, V.62 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:V.62 Water bridges: D:V.62 ACT.8: 2 residues within 4Å: Chain D: E.206, H.207 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:H.207 ACT.9: 5 residues within 4Å: Chain E: G.79, G.80, Q.99, K.114, D.154 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:G.80, E:Q.99 Water bridges: E:Q.99 Salt bridges: E:K.114 ACT.10: 4 residues within 4Å: Chain E: D.252, S.253, K.279, Q.284 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:S.253, E:Q.284 Salt bridges: E:K.279 ACT.11: 2 residues within 4Å: Chain F: V.60, V.62 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:V.62 Water bridges: F:V.62 ACT.12: 2 residues within 4Å: Chain F: E.206, H.207 1 PLIP interactions: 1 interactions with chain F Salt bridges: F:H.207

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Godsora, B.K.J. et al., Conformational flexibility associated with remote residues regulates the kinetic properties of glutamate dehydrogenase. Protein Sci. (2025)

Release Date

2025-03-05

Peptides

Glutamate dehydrogenase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

C
B

D
A

E
B

F
A

Glutamate dehydrogenase

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