SMTL ID : 9kl6.1

Crystal structure of NADP-specific glutamate dehydrogenase Gdh1 from Schizosaccharomyces pombe in complex with alpha-iminoglutarate and NADP+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-hexamer

Ligands

6 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.1: 27 residues within 4Å: Chain A: R.102, H.104, K.142, G.173, D.174, I.175, G.176, R.213, T.217, G.248, S.249, G.250, N.251, V.252, S.271, D.272, S.273, K.297, C.334, A.335, T.336, G.359, S.360, N.361, N.391 Ligands: 2IT.3, GOL.5 33 PLIP interactions: 33 interactions with chain A Hydrophobic interactions: A:T.217, A:V.252, A:N.391 Hydrogen bonds: A:R.102, A:H.104, A:D.174, A:G.176, A:R.213, A:R.213, A:S.249, A:N.251, A:N.251, A:V.252, A:S.273, A:S.273, A:A.335, A:N.361, A:N.361 Water bridges: A:R.102, A:K.142, A:K.142, A:T.217, A:G.250, A:A.253, A:S.273, A:S.273, A:K.297, A:K.297, A:K.297, A:K.297, A:Q.337 Salt bridges: A:K.142, A:K.297 NAP.6: 27 residues within 4Å: Chain B: R.102, H.104, K.142, G.173, D.174, I.175, G.176, R.213, T.217, G.248, S.249, G.250, N.251, V.252, S.271, D.272, S.273, K.297, C.334, A.335, T.336, G.359, S.360, N.361, N.391 Ligands: 2IT.8, GOL.10 33 PLIP interactions: 33 interactions with chain B Hydrophobic interactions: B:T.217, B:V.252, B:N.391 Hydrogen bonds: B:R.102, B:H.104, B:D.174, B:G.176, B:R.213, B:R.213, B:S.249, B:N.251, B:N.251, B:V.252, B:S.273, B:S.273, B:A.335, B:N.361, B:N.361 Water bridges: B:R.102, B:K.142, B:K.142, B:T.217, B:G.250, B:A.253, B:S.273, B:S.273, B:K.297, B:K.297, B:K.297, B:K.297, B:Q.337 Salt bridges: B:K.142, B:K.297 NAP.11: 27 residues within 4Å: Chain C: R.102, H.104, K.142, G.173, D.174, I.175, G.176, R.213, T.217, G.248, S.249, G.250, N.251, V.252, S.271, D.272, S.273, K.297, C.334, A.335, T.336, G.359, S.360, N.361, N.391 Ligands: 2IT.13, GOL.15 33 PLIP interactions: 33 interactions with chain C Hydrophobic interactions: C:T.217, C:V.252, C:N.391 Hydrogen bonds: C:R.102, C:H.104, C:D.174, C:G.176, C:R.213, C:R.213, C:S.249, C:N.251, C:N.251, C:V.252, C:S.273, C:S.273, C:A.335, C:N.361, C:N.361 Water bridges: C:R.102, C:K.142, C:K.142, C:T.217, C:G.250, C:A.253, C:S.273, C:S.273, C:K.297, C:K.297, C:K.297, C:K.297, C:Q.337 Salt bridges: C:K.142, C:K.297 NAP.16: 27 residues within 4Å: Chain D: R.102, H.104, K.142, G.173, D.174, I.175, G.176, R.213, T.217, G.248, S.249, G.250, N.251, V.252, S.271, D.272, S.273, K.297, C.334, A.335, T.336, G.359, S.360, N.361, N.391 Ligands: 2IT.18, GOL.20 34 PLIP interactions: 34 interactions with chain D Hydrophobic interactions: D:T.217, D:V.252, D:N.391 Hydrogen bonds: D:R.102, D:H.104, D:D.174, D:G.176, D:R.213, D:R.213, D:T.217, D:S.249, D:N.251, D:N.251, D:V.252, D:S.273, D:S.273, D:A.335, D:T.336, D:N.361, D:N.361 Water bridges: D:R.102, D:K.142, D:K.142, D:G.250, D:A.253, D:S.273, D:S.273, D:K.297, D:K.297, D:K.297, D:K.297, D:Q.337 Salt bridges: D:K.142, D:K.297 NAP.21: 27 residues within 4Å: Chain E: R.102, H.104, K.142, G.173, D.174, I.175, G.176, R.213, T.217, G.248, S.249, G.250, N.251, V.252, S.271, D.272, S.273, K.297, C.334, A.335, T.336, G.359, S.360, N.361, N.391 Ligands: 2IT.23, GOL.25 34 PLIP interactions: 34 interactions with chain E Hydrophobic interactions: E:T.217, E:V.252, E:N.391 Hydrogen bonds: E:R.102, E:H.104, E:D.174, E:G.176, E:R.213, E:R.213, E:T.217, E:S.249, E:N.251, E:N.251, E:V.252, E:S.273, E:S.273, E:A.335, E:T.336, E:N.361, E:N.361 Water bridges: E:R.102, E:K.142, E:K.142, E:G.250, E:A.253, E:S.273, E:S.273, E:K.297, E:K.297, E:K.297, E:K.297, E:Q.337 Salt bridges: E:K.142, E:K.297 NAP.26: 27 residues within 4Å: Chain F: R.102, H.104, K.142, G.173, D.174, I.175, G.176, R.213, T.217, G.248, S.249, G.250, N.251, V.252, S.271, D.272, S.273, K.297, C.334, A.335, T.336, G.359, S.360, N.361, N.391 Ligands: 2IT.28, GOL.30 34 PLIP interactions: 34 interactions with chain F Hydrophobic interactions: F:T.217, F:V.252, F:N.391 Hydrogen bonds: F:R.102, F:H.104, F:D.174, F:G.176, F:R.213, F:R.213, F:T.217, F:S.249, F:N.251, F:N.251, F:V.252, F:S.273, F:S.273, F:A.335, F:T.336, F:N.361, F:N.361 Water bridges: F:R.102, F:K.142, F:K.142, F:G.250, F:A.253, F:S.273, F:S.273, F:K.297, F:K.297, F:K.297, F:K.297, F:Q.337 Salt bridges: F:K.142, F:K.297

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 4 residues within 4Å: Chain A: I.349, S.375, G.379, E.380 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.380 Water bridges: A:E.380, A:E.380 SO4.7: 4 residues within 4Å: Chain B: I.349, S.375, G.379, E.380 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.380 Water bridges: B:E.380, B:E.380 SO4.12: 4 residues within 4Å: Chain C: I.349, S.375, G.379, E.380 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.380 Water bridges: C:E.380, C:E.380 SO4.17: 4 residues within 4Å: Chain D: I.349, S.375, G.379, E.380 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:E.380 Water bridges: D:E.380 SO4.22: 4 residues within 4Å: Chain E: I.349, S.375, G.379, E.380 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:E.380 Water bridges: E:E.380 SO4.27: 4 residues within 4Å: Chain F: I.349, S.375, G.379, E.380 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:E.380 Water bridges: F:E.380

6 x 2IT: (2Z)-2-iminopentanedioic acid(Non-covalent)

2IT.3: 15 residues within 4Å: Chain A: K.98, G.99, G.100, Q.119, K.122, K.134, A.172, G.173, D.174, R.213, N.361, G.394, V.395, S.398 Ligands: NAP.1 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:A.172 Hydrogen bonds: A:Q.119, A:K.134, A:D.174, A:D.174, A:T.201, A:N.361, A:G.394, A:S.398 Water bridges: A:K.122 Salt bridges: A:K.98, A:K.122, A:K.134, A:R.213 2IT.8: 15 residues within 4Å: Chain B: K.98, G.99, G.100, Q.119, K.122, K.134, A.172, G.173, D.174, R.213, N.361, G.394, V.395, S.398 Ligands: NAP.6 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:A.172 Hydrogen bonds: B:Q.119, B:K.134, B:D.174, B:D.174, B:T.201, B:N.361, B:G.394, B:S.398 Water bridges: B:K.122 Salt bridges: B:K.98, B:K.122, B:K.134, B:R.213 2IT.13: 15 residues within 4Å: Chain C: K.98, G.99, G.100, Q.119, K.122, K.134, A.172, G.173, D.174, R.213, N.361, G.394, V.395, S.398 Ligands: NAP.11 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:A.172 Hydrogen bonds: C:Q.119, C:K.134, C:D.174, C:D.174, C:T.201, C:N.361, C:G.394, C:S.398 Water bridges: C:K.122 Salt bridges: C:K.98, C:K.122, C:K.134, C:R.213 2IT.18: 15 residues within 4Å: Chain D: K.98, G.99, G.100, Q.119, K.122, K.134, A.172, G.173, D.174, R.213, N.361, G.394, V.395, S.398 Ligands: NAP.16 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:A.172 Hydrogen bonds: D:Q.119, D:K.134, D:D.174, D:D.174, D:D.174, D:T.201, D:N.361, D:G.394, D:S.398 Water bridges: D:K.122 Salt bridges: D:K.98, D:K.122, D:K.134, D:R.213 2IT.23: 15 residues within 4Å: Chain E: K.98, G.99, G.100, Q.119, K.122, K.134, A.172, G.173, D.174, R.213, N.361, G.394, V.395, S.398 Ligands: NAP.21 15 PLIP interactions: 15 interactions with chain E Hydrophobic interactions: E:A.172 Hydrogen bonds: E:Q.119, E:K.134, E:D.174, E:D.174, E:D.174, E:T.201, E:N.361, E:G.394, E:S.398 Water bridges: E:K.122 Salt bridges: E:K.98, E:K.122, E:K.134, E:R.213 2IT.28: 15 residues within 4Å: Chain F: K.98, G.99, G.100, Q.119, K.122, K.134, A.172, G.173, D.174, R.213, N.361, G.394, V.395, S.398 Ligands: NAP.26 15 PLIP interactions: 15 interactions with chain F Hydrophobic interactions: F:A.172 Hydrogen bonds: F:Q.119, F:K.134, F:D.174, F:D.174, F:D.174, F:T.201, F:N.361, F:G.394, F:S.398 Water bridges: F:K.122 Salt bridges: F:K.98, F:K.122, F:K.134, F:R.213

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 8 residues within 4Å: Chain A: S.92, Y.97, T.168 Chain B: K.190, R.191, N.194, E.195, Y.196 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.92, A:T.168, B:K.190 Water bridges: A:R.65, B:R.191 GOL.5: 5 residues within 4Å: Chain A: A.172, G.173, G.202, R.213 Ligands: NAP.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.173 Water bridges: A:G.173, A:V.177, A:G.179 GOL.9: 8 residues within 4Å: Chain B: S.92, Y.97, T.168 Chain C: K.190, R.191, N.194, E.195, Y.196 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:K.190, B:S.92, B:T.168 Water bridges: C:R.191, B:R.65 GOL.10: 5 residues within 4Å: Chain B: A.172, G.173, G.202, R.213 Ligands: NAP.6 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.173 Water bridges: B:G.173, B:V.177, B:G.179 GOL.14: 8 residues within 4Å: Chain A: K.190, R.191, N.194, E.195, Y.196 Chain C: S.92, Y.97, T.168 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:S.92, C:T.168, A:K.190 Water bridges: C:R.65, A:R.191 GOL.15: 5 residues within 4Å: Chain C: A.172, G.173, G.202, R.213 Ligands: NAP.11 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:G.173 Water bridges: C:G.173, C:V.177, C:G.179 GOL.19: 8 residues within 4Å: Chain D: S.92, Y.97, T.168 Chain E: K.190, R.191, N.194, E.195, Y.196 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain E Hydrogen bonds: D:S.92, D:T.168, E:K.190 Water bridges: D:R.65, E:R.191 GOL.20: 5 residues within 4Å: Chain D: A.172, G.173, G.202, R.213 Ligands: NAP.16 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:G.173 Water bridges: D:G.173, D:V.177, D:G.179 GOL.24: 8 residues within 4Å: Chain E: S.92, Y.97, T.168 Chain F: K.190, R.191, N.194, E.195, Y.196 5 PLIP interactions: 3 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:S.92, E:T.168, F:K.190 Water bridges: E:R.65, F:R.191 GOL.25: 5 residues within 4Å: Chain E: A.172, G.173, G.202, R.213 Ligands: NAP.21 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:G.173 Water bridges: E:G.173, E:V.177, E:G.179 GOL.29: 8 residues within 4Å: Chain D: K.190, R.191, N.194, E.195, Y.196 Chain F: S.92, Y.97, T.168 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain F Hydrogen bonds: D:K.190, F:S.92, F:T.168 Water bridges: D:R.191, F:R.65 GOL.30: 5 residues within 4Å: Chain F: A.172, G.173, G.202, R.213 Ligands: NAP.26 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:G.173 Water bridges: F:G.173, F:V.177, F:G.179

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, Y.F. et al., Phosphorylation-mediated regulation of the NADPH-dependent glutamate dehydrogenase, SpGdh1, from Schizosaccharomyces pombe. J.Biol.Chem. (2025)

Release Date

2025-07-30

Peptides

NADP-specific glutamate dehydrogenase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

NADP-specific glutamate dehydrogenase