SMTL ID : 7f79.1

Crystal structure of glutamate dehydrogenase 3 from Candida albicans in complex with alpha-ketoglutarate and NADPH

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-hexamer

Ligands

6 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.1: 25 residues within 4Å: Chain A: R.101, H.103, K.141, D.173, I.174, G.175, R.212, T.216, G.247, S.248, G.249, N.250, V.251, S.270, D.271, S.272, K.294, A.339, T.340, G.363, S.364, N.365, N.394 Ligands: AKG.2, GOL.3 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:T.216 Hydrogen bonds: A:R.101, A:H.103, A:D.173, A:G.175, A:R.212, A:R.212, A:T.216, A:S.248, A:S.248, A:N.250, A:N.250, A:V.251, A:D.271, A:S.272, A:A.339, A:N.365, A:N.365 Salt bridges: A:K.141, A:K.294 NDP.4: 24 residues within 4Å: Chain B: R.101, H.103, K.141, D.173, I.174, G.175, R.212, T.216, S.248, G.249, N.250, V.251, S.270, D.271, S.272, K.294, A.339, T.340, G.363, S.364, N.365, N.394 Ligands: AKG.5, GOL.6 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:T.216, B:N.394 Hydrogen bonds: B:R.101, B:H.103, B:D.173, B:G.175, B:R.212, B:R.212, B:T.216, B:S.248, B:S.248, B:N.250, B:N.250, B:V.251, B:S.272, B:S.272, B:A.339, B:T.340, B:N.365, B:N.365 Salt bridges: B:K.141, B:K.294 NDP.7: 25 residues within 4Å: Chain C: R.101, H.103, K.141, D.173, I.174, G.175, R.212, T.216, G.247, S.248, G.249, N.250, V.251, S.270, D.271, S.272, K.294, S.338, A.339, T.340, G.363, S.364, N.365, N.394 Ligands: AKG.8 21 PLIP interactions: 21 interactions with chain C Hydrophobic interactions: C:T.216, C:N.394 Hydrogen bonds: C:R.101, C:H.103, C:D.173, C:G.175, C:R.212, C:R.212, C:T.216, C:S.248, C:S.248, C:N.250, C:N.250, C:V.251, C:D.271, C:S.272, C:A.339, C:N.365, C:N.365 Salt bridges: C:K.141, C:K.294 NDP.9: 24 residues within 4Å: Chain D: R.101, H.103, K.141, D.173, I.174, G.175, R.212, T.216, G.247, S.248, G.249, N.250, V.251, D.271, S.272, K.294, A.339, T.340, G.363, S.364, N.365, N.394 Ligands: AKG.10, GOL.11 18 PLIP interactions: 18 interactions with chain D Hydrophobic interactions: D:T.216 Hydrogen bonds: D:R.101, D:H.103, D:D.173, D:G.175, D:R.212, D:R.212, D:T.216, D:S.248, D:N.250, D:N.250, D:V.251, D:S.272, D:S.272, D:N.365, D:N.365 Salt bridges: D:K.141, D:K.294 NDP.13: 24 residues within 4Å: Chain E: R.101, K.141, D.173, I.174, G.175, R.212, T.216, G.247, S.248, G.249, N.250, V.251, S.270, D.271, S.272, K.294, A.339, T.340, G.363, S.364, N.365, N.394 Ligands: AKG.14, GOL.15 20 PLIP interactions: 20 interactions with chain E Hydrophobic interactions: E:T.216, E:N.394 Hydrogen bonds: E:R.101, E:D.173, E:G.175, E:R.212, E:R.212, E:S.248, E:S.248, E:N.250, E:N.250, E:V.251, E:D.271, E:S.272, E:S.272, E:A.339, E:N.365, E:N.365 Salt bridges: E:K.141, E:K.294 NDP.16: 22 residues within 4Å: Chain F: R.101, H.103, K.141, D.173, I.174, G.175, R.212, T.216, S.248, G.249, N.250, V.251, D.271, S.272, K.294, A.339, T.340, G.363, S.364, N.365, N.394 Ligands: AKG.17 17 PLIP interactions: 17 interactions with chain F Hydrophobic interactions: F:T.216 Hydrogen bonds: F:R.101, F:H.103, F:D.173, F:G.175, F:R.212, F:R.212, F:S.248, F:N.250, F:N.250, F:V.251, F:S.272, F:A.339, F:N.365, F:N.365 Salt bridges: F:K.141, F:K.294

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

AKG.2: 15 residues within 4Å: Chain A: K.97, G.98, G.99, Q.118, K.121, K.133, A.171, G.172, D.173, R.212, N.365, G.397, V.398, S.401 Ligands: NDP.1 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:V.398 Hydrogen bonds: A:G.98, A:G.99, A:Q.118, A:K.133, A:D.173, A:N.365, A:S.401 Salt bridges: A:K.97, A:K.121, A:K.133, A:R.212 AKG.5: 14 residues within 4Å: Chain B: K.97, G.99, Q.118, K.121, K.133, A.171, D.173, R.212, N.365, N.394, G.397, V.398, S.401 Ligands: NDP.4 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:G.99, B:Q.118, B:D.173, B:N.365, B:V.398, B:S.401 Salt bridges: B:K.97, B:K.121, B:K.133, B:R.212 AKG.8: 16 residues within 4Å: Chain C: K.97, G.98, G.99, Q.118, K.121, K.133, A.171, G.172, D.173, T.200, R.212, N.365, G.397, V.398, S.401 Ligands: NDP.7 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:G.98, C:Q.118, C:K.133, C:T.200, C:N.365, C:V.398, C:S.401 Salt bridges: C:K.97, C:K.121, C:K.133, C:R.212 AKG.10: 16 residues within 4Å: Chain D: K.97, G.98, G.99, Q.118, K.121, K.133, A.171, G.172, D.173, T.200, R.212, N.365, G.397, V.398, S.401 Ligands: NDP.9 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:V.398 Hydrogen bonds: D:G.99, D:Q.118, D:K.133, D:D.173, D:N.365, D:S.401 Salt bridges: D:K.97, D:K.121, D:K.133, D:R.212 AKG.14: 16 residues within 4Å: Chain E: K.97, G.98, G.99, Q.118, K.121, K.133, A.171, G.172, D.173, T.200, R.212, N.365, G.397, V.398, S.401 Ligands: NDP.13 10 PLIP interactions: 10 interactions with chain E Hydrophobic interactions: E:V.398 Hydrogen bonds: E:G.99, E:Q.118, E:T.200, E:N.365, E:S.401 Salt bridges: E:K.97, E:K.121, E:K.133, E:R.212 AKG.17: 16 residues within 4Å: Chain F: K.97, G.98, G.99, Q.118, K.121, K.133, V.169, A.171, G.172, D.173, T.200, R.212, N.365, V.398, S.401 Ligands: NDP.16 13 PLIP interactions: 13 interactions with chain F Hydrophobic interactions: F:V.398 Hydrogen bonds: F:G.98, F:Q.118, F:K.133, F:D.173, F:T.200, F:N.365, F:S.401 Water bridges: F:K.121 Salt bridges: F:K.97, F:K.121, F:K.133, F:R.212

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: G.172, V.176, R.212, P.213, N.250 Ligands: NDP.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.172, A:V.176, A:R.212 GOL.6: 6 residues within 4Å: Chain B: G.172, V.181, G.201, R.212, N.250 Ligands: NDP.4 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.172, B:G.201, B:N.250 GOL.11: 7 residues within 4Å: Chain D: G.172, V.181, G.201, R.212, P.213, N.250 Ligands: NDP.9 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:G.201, D:R.212 GOL.12: 5 residues within 4Å: Chain D: G.126, L.127, S.128 Chain F: R.411, Q.413 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain F Hydrogen bonds: D:S.128, F:Q.413 GOL.15: 7 residues within 4Å: Chain E: G.172, D.173, V.176, G.201, R.212, N.250 Ligands: NDP.13 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:G.172, E:D.173

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, N. et al., Crystal structure of glutamate dehydrogenase 3 from Candida albicans. Biochem.Biophys.Res.Commun. (2021)

Release Date

2021-07-21

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

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