SMTL ID : 8c53.1

Trypanosoma brucei IMP dehydrogenase (ori) crystallized in High Five cells reveals native ligands ATP, GDP and phosphate. Diffraction data collection at 100 K in cellulo; CrystFEL processing

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-octamer

Ligands

8 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)(Covalent)

GDP.1: 17 residues within 4Å: Chain A: R.98, R.101, L.105, N.108, I.111, K.113, P.114, K.115, K.133, I.135, S.136, G.137, I.138, L.139, Y.202, L.215, S.217 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:R.98, A:N.108, A:K.115, A:S.136, A:G.137 Water bridges: A:R.223 Salt bridges: A:R.101, A:K.115, A:K.133, A:K.133 GDP.4: 17 residues within 4Å: Chain B: R.98, R.101, L.105, N.108, I.111, K.113, P.114, K.115, K.133, I.135, S.136, G.137, I.138, L.139, Y.202, L.215, S.217 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:K.113, B:K.115, B:G.137, B:G.137, B:L.139 Water bridges: B:R.223 Salt bridges: B:R.101, B:K.115, B:K.133, B:K.133 GDP.7: 17 residues within 4Å: Chain C: R.98, R.101, L.105, N.108, I.111, K.113, P.114, K.115, K.133, I.135, S.136, G.137, I.138, L.139, Y.202, L.215, S.217 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:R.98, C:N.108, C:K.115, C:S.136, C:G.137 Water bridges: C:R.223 Salt bridges: C:R.101, C:K.115, C:K.133, C:K.133 GDP.10: 17 residues within 4Å: Chain D: R.98, R.101, L.105, N.108, I.111, K.113, P.114, K.115, K.133, I.135, S.136, G.137, I.138, L.139, Y.202, L.215, S.217 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:K.113, D:K.115, D:G.137, D:G.137, D:L.139 Water bridges: D:R.223 Salt bridges: D:R.101, D:K.115, D:K.133, D:K.133 GDP.13: 17 residues within 4Å: Chain E: R.98, R.101, L.105, N.108, I.111, K.113, P.114, K.115, K.133, I.135, S.136, G.137, I.138, L.139, Y.202, L.215, S.217 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:R.98, E:N.108, E:K.115, E:S.136, E:G.137 Water bridges: E:R.223 Salt bridges: E:R.101, E:K.115, E:K.133, E:K.133 GDP.16: 17 residues within 4Å: Chain F: R.98, R.101, L.105, N.108, I.111, K.113, P.114, K.115, K.133, I.135, S.136, G.137, I.138, L.139, Y.202, L.215, S.217 10 PLIP interactions: 10 interactions with chain F Hydrogen bonds: F:K.113, F:K.115, F:G.137, F:G.137, F:L.139 Water bridges: F:R.223 Salt bridges: F:R.101, F:K.115, F:K.133, F:K.133 GDP.19: 17 residues within 4Å: Chain G: R.98, R.101, L.105, N.108, I.111, K.113, P.114, K.115, K.133, I.135, S.136, G.137, I.138, L.139, Y.202, L.215, S.217 10 PLIP interactions: 10 interactions with chain G Hydrogen bonds: G:R.98, G:N.108, G:K.115, G:S.136, G:G.137 Water bridges: G:R.223 Salt bridges: G:R.101, G:K.115, G:K.133, G:K.133 GDP.22: 17 residues within 4Å: Chain H: R.98, R.101, L.105, N.108, I.111, K.113, P.114, K.115, K.133, I.135, S.136, G.137, I.138, L.139, Y.202, L.215, S.217 10 PLIP interactions: 10 interactions with chain H Hydrogen bonds: H:K.113, H:K.115, H:G.137, H:G.137, H:L.139 Water bridges: H:R.223 Salt bridges: H:R.101, H:K.115, H:K.133, H:K.133

8 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.2: 21 residues within 4Å: Chain A: S.136, I.153, C.155, T.156, K.157, D.158, T.174, N.178, M.179, T.180, V.181, R.199, H.200, G.201, Y.202, L.203, P.204, R.219 Chain B: K.157, R.199 Ligands: ATP.5 19 PLIP interactions: 14 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:S.136, A:T.156, A:T.156, A:T.180, A:T.180, A:G.201 Water bridges: A:K.157, A:K.157, B:K.157, B:K.157 Salt bridges: A:K.157, A:K.157, A:R.219, A:R.219, B:K.157, B:K.157, B:K.157 pi-Stacking: A:H.200, A:H.200 ATP.5: 19 residues within 4Å: Chain A: K.157, R.199 Chain B: S.136, I.153, C.155, T.156, K.157, D.158, T.174, N.178, M.179, T.180, H.200, G.201, Y.202, L.203, P.204, R.219 Ligands: ATP.2 17 PLIP interactions: 13 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:S.136, B:T.180, B:T.180, B:G.201, B:Y.202 Water bridges: B:K.157, B:K.157, B:R.219, A:K.157 Salt bridges: B:K.157, B:K.157, B:R.219, A:K.157, A:K.157, A:K.157 pi-Stacking: B:H.200, B:H.200 ATP.8: 21 residues within 4Å: Chain C: S.136, I.153, C.155, T.156, K.157, D.158, T.174, N.178, M.179, T.180, V.181, R.199, H.200, G.201, Y.202, L.203, P.204, R.219 Chain D: K.157, R.199 Ligands: ATP.11 19 PLIP interactions: 14 interactions with chain C, 5 interactions with chain D Hydrogen bonds: C:S.136, C:T.156, C:T.156, C:T.180, C:T.180, C:G.201 Water bridges: C:K.157, C:K.157, D:K.157, D:K.157 Salt bridges: C:K.157, C:K.157, C:R.219, C:R.219, D:K.157, D:K.157, D:K.157 pi-Stacking: C:H.200, C:H.200 ATP.11: 19 residues within 4Å: Chain C: K.157, R.199 Chain D: S.136, I.153, C.155, T.156, K.157, D.158, T.174, N.178, M.179, T.180, H.200, G.201, Y.202, L.203, P.204, R.219 Ligands: ATP.8 17 PLIP interactions: 13 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:S.136, D:T.180, D:T.180, D:G.201, D:Y.202 Water bridges: D:K.157, D:K.157, D:R.219, C:K.157 Salt bridges: D:K.157, D:K.157, D:R.219, C:K.157, C:K.157, C:K.157 pi-Stacking: D:H.200, D:H.200 ATP.14: 21 residues within 4Å: Chain E: S.136, I.153, C.155, T.156, K.157, D.158, T.174, N.178, M.179, T.180, V.181, R.199, H.200, G.201, Y.202, L.203, P.204, R.219 Chain F: K.157, R.199 Ligands: ATP.17 19 PLIP interactions: 14 interactions with chain E, 5 interactions with chain F Hydrogen bonds: E:S.136, E:T.156, E:T.156, E:T.180, E:T.180, E:G.201 Water bridges: E:K.157, E:K.157, F:K.157, F:K.157 Salt bridges: E:K.157, E:K.157, E:R.219, E:R.219, F:K.157, F:K.157, F:K.157 pi-Stacking: E:H.200, E:H.200 ATP.17: 19 residues within 4Å: Chain E: K.157, R.199 Chain F: S.136, I.153, C.155, T.156, K.157, D.158, T.174, N.178, M.179, T.180, H.200, G.201, Y.202, L.203, P.204, R.219 Ligands: ATP.14 17 PLIP interactions: 13 interactions with chain F, 4 interactions with chain E Hydrogen bonds: F:S.136, F:T.180, F:T.180, F:G.201, F:Y.202 Water bridges: F:K.157, F:K.157, F:R.219, E:K.157 Salt bridges: F:K.157, F:K.157, F:R.219, E:K.157, E:K.157, E:K.157 pi-Stacking: F:H.200, F:H.200 ATP.20: 21 residues within 4Å: Chain G: S.136, I.153, C.155, T.156, K.157, D.158, T.174, N.178, M.179, T.180, V.181, R.199, H.200, G.201, Y.202, L.203, P.204, R.219 Chain H: K.157, R.199 Ligands: ATP.23 19 PLIP interactions: 14 interactions with chain G, 5 interactions with chain H Hydrogen bonds: G:S.136, G:T.156, G:T.156, G:T.180, G:T.180, G:G.201 Water bridges: G:K.157, G:K.157, H:K.157, H:K.157 Salt bridges: G:K.157, G:K.157, G:R.219, G:R.219, H:K.157, H:K.157, H:K.157 pi-Stacking: G:H.200, G:H.200 ATP.23: 19 residues within 4Å: Chain G: K.157, R.199 Chain H: S.136, I.153, C.155, T.156, K.157, D.158, T.174, N.178, M.179, T.180, H.200, G.201, Y.202, L.203, P.204, R.219 Ligands: ATP.20 17 PLIP interactions: 4 interactions with chain G, 13 interactions with chain H Water bridges: G:K.157, H:K.157, H:K.157, H:R.219 Salt bridges: G:K.157, G:K.157, G:K.157, H:K.157, H:K.157, H:R.219 Hydrogen bonds: H:S.136, H:T.180, H:T.180, H:G.201, H:Y.202 pi-Stacking: H:H.200, H:H.200

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

PO4.3: 6 residues within 4Å: Chain A: G.359, G.360, L.361, R.362, G.381, S.382 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.360, A:L.361, A:G.381, A:S.382 Water bridges: A:M.383 PO4.6: 7 residues within 4Å: Chain B: M.66, G.359, G.360, L.361, G.381, S.382, M.383 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.360, B:L.361, B:G.381, B:S.382, B:M.383 PO4.9: 6 residues within 4Å: Chain C: G.359, G.360, L.361, R.362, G.381, S.382 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:G.360, C:L.361, C:G.381, C:S.382 Water bridges: C:M.383 PO4.12: 7 residues within 4Å: Chain D: M.66, G.359, G.360, L.361, G.381, S.382, M.383 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:G.360, D:L.361, D:G.381, D:S.382, D:M.383 PO4.15: 6 residues within 4Å: Chain E: G.359, G.360, L.361, R.362, G.381, S.382 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:G.360, E:L.361, E:G.381, E:S.382 Water bridges: E:M.383 PO4.18: 7 residues within 4Å: Chain F: M.66, G.359, G.360, L.361, G.381, S.382, M.383 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:G.360, F:L.361, F:G.381, F:S.382, F:M.383 PO4.21: 6 residues within 4Å: Chain G: G.359, G.360, L.361, R.362, G.381, S.382 5 PLIP interactions: 5 interactions with chain G Hydrogen bonds: G:G.360, G:L.361, G:G.381, G:S.382 Water bridges: G:M.383 PO4.24: 7 residues within 4Å: Chain H: M.66, G.359, G.360, L.361, G.381, S.382, M.383 5 PLIP interactions: 5 interactions with chain H Hydrogen bonds: H:G.360, H:L.361, H:G.381, H:S.382, H:M.383

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schonherr, R. et al., A streamlined approach to structure elucidation using in cellulo crystallized recombinant proteins, InCellCryst. Nat Commun (2024)

Release Date

2024-01-17

Peptides

Inosine-5'-monophosphate dehydrogenase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

G
A

H
B

Inosine-5'-monophosphate dehydrogenase

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