SMTL ID : 6g2u.1

Crystal structure of the human glutamate dehydrogenase 2 (hGDH2)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.93 Å

Oligo State

homo-hexamer

Ligands

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

PO4.1: 4 residues within 4Å: Chain A: S.397, R.400 Chain D: D.123, R.463 Ligand excluded by PLIP PO4.2: 4 residues within 4Å: Chain A: R.221, Y.266, R.269, K.450 Ligand excluded by PLIP PO4.3: 3 residues within 4Å: Chain A: N.394 Chain B: N.394 Chain D: N.394 Ligand excluded by PLIP PO4.4: 4 residues within 4Å: Chain A: H.213, G.214, R.215, K.450 Ligand excluded by PLIP PO4.10: 3 residues within 4Å: Chain A: R.463 Chain B: S.397, R.400 Ligand excluded by PLIP PO4.11: 5 residues within 4Å: Chain B: R.221, R.265, Y.266, R.269, H.454 Ligand excluded by PLIP PO4.12: 5 residues within 4Å: Chain A: T.431 Chain B: R.423, K.424 Chain E: R.247, D.248 Ligand excluded by PLIP PO4.13: 1 residues within 4Å: Chain B: Y.194 Ligand excluded by PLIP PO4.14: 3 residues within 4Å: Chain B: H.213, G.214, K.450 Ligand excluded by PLIP PO4.17: 4 residues within 4Å: Chain C: D.123, R.463 Chain F: S.397, R.400 Ligand excluded by PLIP PO4.18: 5 residues within 4Å: Chain C: R.221, R.265, Y.266, R.269, K.450 Ligand excluded by PLIP PO4.19: 2 residues within 4Å: Chain C: S.397, R.400 Ligand excluded by PLIP PO4.20: 1 residues within 4Å: Ligands: NA.22 Ligand excluded by PLIP PO4.21: 1 residues within 4Å: Chain C: K.293 Ligand excluded by PLIP PO4.26: 4 residues within 4Å: Chain B: D.123, R.463 Chain D: S.397, R.400 Ligand excluded by PLIP PO4.27: 4 residues within 4Å: Chain D: R.221, R.265, Y.266, R.269 Ligand excluded by PLIP PO4.44: 3 residues within 4Å: Chain E: H.213, G.214, K.450 Ligand excluded by PLIP PO4.45: 6 residues within 4Å: Chain E: S.217, R.221, R.265, Y.266, R.269, K.450 Ligand excluded by PLIP PO4.55: 3 residues within 4Å: Chain F: H.213, G.214, K.450 Ligand excluded by PLIP PO4.56: 6 residues within 4Å: Chain F: S.217, R.221, R.265, Y.266, R.269, K.450 Ligand excluded by PLIP PO4.57: 2 residues within 4Å: Chain F: D.123, R.463 Ligand excluded by PLIP PO4.58: 2 residues within 4Å: Chain C: N.394 Chain F: N.394 Ligand excluded by PLIP PO4.59: 1 residues within 4Å: Chain F: Y.194 Ligand excluded by PLIP

21 x NA: SODIUM ION(Non-functional Binders)

NA.5: 2 residues within 4Å: Chain A: A.472, G.478 Ligand excluded by PLIP NA.6: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP NA.22: 3 residues within 4Å: Chain C: E.419, R.423 Ligands: PO4.20 Ligand excluded by PLIP NA.23: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP NA.28: 5 residues within 4Å: Chain D: I.55, I.56, P.58, N.60, H.86 Ligand excluded by PLIP NA.29: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP NA.30: 1 residues within 4Å: Chain D: K.344 Ligand excluded by PLIP NA.31: 1 residues within 4Å: Ligands: CL.43 Ligand excluded by PLIP NA.32: 1 residues within 4Å: Chain D: H.470 Ligand excluded by PLIP NA.33: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP NA.34: 1 residues within 4Å: Chain D: N.136 Ligand excluded by PLIP NA.35: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP NA.36: 2 residues within 4Å: Chain D: Y.194, D.195 Ligand excluded by PLIP NA.37: 2 residues within 4Å: Chain D: D.172, T.175 Ligand excluded by PLIP NA.38: 5 residues within 4Å: Chain A: L.393 Chain B: L.393, N.394 Chain D: L.393, N.394 Ligand excluded by PLIP NA.46: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP NA.47: 4 residues within 4Å: Chain E: P.11, T.357, P.358, E.359 Ligand excluded by PLIP NA.48: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP NA.60: 1 residues within 4Å: Chain F: N.392 Ligand excluded by PLIP NA.61: 2 residues within 4Å: Chain F: E.146, R.150 Ligand excluded by PLIP NA.62: 4 residues within 4Å: Chain C: T.91 Chain F: H.193, D.195, A.198 Ligand excluded by PLIP

19 x CL: CHLORIDE ION(Non-functional Binders)

CL.7: 1 residues within 4Å: Chain A: R.247 Ligand excluded by PLIP CL.8: 1 residues within 4Å: Chain A: R.70 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain A: V.33, E.42, R.46 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain A: N.197 Chain B: N.197 Chain D: N.197 Ligand excluded by PLIP CL.16: 2 residues within 4Å: Chain B: N.47, R.50 Ligand excluded by PLIP CL.24: 3 residues within 4Å: Chain C: H.213, G.214, K.450 Ligand excluded by PLIP CL.25: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.39: 1 residues within 4Å: Chain D: H.268 Ligand excluded by PLIP CL.40: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.41: 1 residues within 4Å: Chain D: S.64 Ligand excluded by PLIP CL.42: 1 residues within 4Å: Chain D: D.281 Ligand excluded by PLIP CL.43: 2 residues within 4Å: Chain D: H.470 Ligands: NA.31 Ligand excluded by PLIP CL.49: 1 residues within 4Å: Chain E: D.10 Ligand excluded by PLIP CL.50: 1 residues within 4Å: Chain E: G.478 Ligand excluded by PLIP CL.51: 2 residues within 4Å: Chain E: K.147, R.151 Ligand excluded by PLIP CL.52: 1 residues within 4Å: Chain E: R.367 Ligand excluded by PLIP CL.53: 2 residues within 4Å: Chain E: G.429, G.430 Ligand excluded by PLIP CL.54: 1 residues within 4Å: Chain E: L.393 Ligand excluded by PLIP CL.63: 2 residues within 4Å: Chain F: G.19, R.23 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dimovasili, C. et al., Crystal structure of glutamate dehydrogenase 2, a positively selected novel human enzyme involved in brain biology and cancer pathophysiology. J.Neurochem. (2021)

Release Date

2019-04-10

Peptides

Glutamate dehydrogenase 2, mitochondrial: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Glutamate dehydrogenase 2, mitochondrial