SMTL ID : 8c51.1

Trypanosoma brucei IMP dehydrogenase (cyto) crystallized in High Five cells revealing native ligands ATP, GDP and phosphate. Diffraction data collection at 100 K in cellulo

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-octamer

Ligands

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

GDP.1: 18 residues within 4Å: Chain A: R.99, R.102, L.106, N.109, I.112, M.113, K.114, P.115, K.116, K.134, I.136, S.137, G.138, I.139, L.140, Y.203, L.216, S.218 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:R.102, A:K.116, A:S.137, A:G.138, A:Y.203 Salt bridges: A:R.99, A:K.116, A:K.116, A:K.134, A:K.134 GDP.5: 17 residues within 4Å: Chain B: R.99, R.102, L.106, N.109, I.112, K.114, P.115, K.116, K.134, I.136, S.137, G.138, I.139, L.140, Y.203, L.216, S.218 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:K.114, B:K.116, B:G.138, B:G.138, B:L.140 Salt bridges: B:R.99, B:R.102, B:K.116, B:K.116, B:K.134, B:K.134 GDP.7: 18 residues within 4Å: Chain C: R.99, R.102, L.106, N.109, I.112, M.113, K.114, P.115, K.116, K.134, I.136, S.137, G.138, I.139, L.140, Y.203, L.216, S.218 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:R.102, C:K.116, C:S.137, C:G.138, C:Y.203 Salt bridges: C:R.99, C:K.116, C:K.116, C:K.134, C:K.134 GDP.11: 17 residues within 4Å: Chain D: R.99, R.102, L.106, N.109, I.112, K.114, P.115, K.116, K.134, I.136, S.137, G.138, I.139, L.140, Y.203, L.216, S.218 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:K.114, D:K.116, D:G.138, D:G.138, D:L.140 Salt bridges: D:R.99, D:R.102, D:K.116, D:K.116, D:K.134, D:K.134 GDP.13: 18 residues within 4Å: Chain E: R.99, R.102, L.106, N.109, I.112, M.113, K.114, P.115, K.116, K.134, I.136, S.137, G.138, I.139, L.140, Y.203, L.216, S.218 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:R.102, E:K.116, E:S.137, E:G.138, E:Y.203 Salt bridges: E:R.99, E:K.116, E:K.116, E:K.134, E:K.134 GDP.17: 17 residues within 4Å: Chain F: R.99, R.102, L.106, N.109, I.112, K.114, P.115, K.116, K.134, I.136, S.137, G.138, I.139, L.140, Y.203, L.216, S.218 11 PLIP interactions: 11 interactions with chain F Hydrogen bonds: F:K.114, F:K.116, F:G.138, F:G.138, F:L.140 Salt bridges: F:R.99, F:R.102, F:K.116, F:K.116, F:K.134, F:K.134 GDP.19: 18 residues within 4Å: Chain G: R.99, R.102, L.106, N.109, I.112, M.113, K.114, P.115, K.116, K.134, I.136, S.137, G.138, I.139, L.140, Y.203, L.216, S.218 10 PLIP interactions: 10 interactions with chain G Hydrogen bonds: G:R.102, G:K.116, G:S.137, G:G.138, G:Y.203 Salt bridges: G:R.99, G:K.116, G:K.116, G:K.134, G:K.134 GDP.23: 17 residues within 4Å: Chain H: R.99, R.102, L.106, N.109, I.112, K.114, P.115, K.116, K.134, I.136, S.137, G.138, I.139, L.140, Y.203, L.216, S.218 11 PLIP interactions: 11 interactions with chain H Hydrogen bonds: H:K.114, H:K.116, H:G.138, H:G.138, H:L.140 Salt bridges: H:R.99, H:R.102, H:K.116, H:K.116, H:K.134, H:K.134

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

ATP.2: 19 residues within 4Å: Chain A: I.154, C.156, T.157, K.158, D.159, T.175, N.179, M.180, T.181, V.182, H.201, G.202, Y.203, L.204, P.205, R.220 Chain B: K.158, R.200 Ligands: ATP.4 20 PLIP interactions: 17 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:T.157, A:T.157, A:T.157, A:K.158, A:D.159, A:D.159, A:T.175, A:T.181, A:T.181, A:H.201, A:G.202, A:Y.203 Salt bridges: A:K.158, A:R.220, A:R.220, B:K.158, B:K.158, B:K.158 pi-Stacking: A:H.201, A:H.201 ATP.4: 19 residues within 4Å: Chain A: K.158, R.200 Chain B: S.137, I.154, C.156, T.157, K.158, D.159, T.175, N.179, M.180, T.181, H.201, G.202, Y.203, L.204, P.205, R.220 Ligands: ATP.2 19 PLIP interactions: 16 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:S.137, B:T.157, B:T.157, B:D.159, B:D.159, B:T.175, B:T.181, B:T.181, B:H.201, B:G.202, B:Y.203 Salt bridges: B:K.158, B:K.158, B:R.220, B:R.220, A:K.158, A:K.158, A:K.158 pi-Stacking: B:H.201 ATP.8: 19 residues within 4Å: Chain C: I.154, C.156, T.157, K.158, D.159, T.175, N.179, M.180, T.181, V.182, H.201, G.202, Y.203, L.204, P.205, R.220 Chain D: K.158, R.200 Ligands: ATP.10 20 PLIP interactions: 17 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:T.157, C:T.157, C:T.157, C:K.158, C:D.159, C:D.159, C:T.175, C:T.181, C:T.181, C:H.201, C:G.202, C:Y.203 Salt bridges: C:K.158, C:R.220, C:R.220, D:K.158, D:K.158, D:K.158 pi-Stacking: C:H.201, C:H.201 ATP.10: 19 residues within 4Å: Chain C: K.158, R.200 Chain D: S.137, I.154, C.156, T.157, K.158, D.159, T.175, N.179, M.180, T.181, H.201, G.202, Y.203, L.204, P.205, R.220 Ligands: ATP.8 19 PLIP interactions: 16 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:S.137, D:T.157, D:T.157, D:D.159, D:D.159, D:T.175, D:T.181, D:T.181, D:H.201, D:G.202, D:Y.203 Salt bridges: D:K.158, D:K.158, D:R.220, D:R.220, C:K.158, C:K.158, C:K.158 pi-Stacking: D:H.201 ATP.14: 19 residues within 4Å: Chain E: I.154, C.156, T.157, K.158, D.159, T.175, N.179, M.180, T.181, V.182, H.201, G.202, Y.203, L.204, P.205, R.220 Chain F: K.158, R.200 Ligands: ATP.16 20 PLIP interactions: 17 interactions with chain E, 3 interactions with chain F Hydrogen bonds: E:T.157, E:T.157, E:T.157, E:K.158, E:D.159, E:D.159, E:T.175, E:T.181, E:T.181, E:H.201, E:G.202, E:Y.203 Salt bridges: E:K.158, E:R.220, E:R.220, F:K.158, F:K.158, F:K.158 pi-Stacking: E:H.201, E:H.201 ATP.16: 19 residues within 4Å: Chain E: K.158, R.200 Chain F: S.137, I.154, C.156, T.157, K.158, D.159, T.175, N.179, M.180, T.181, H.201, G.202, Y.203, L.204, P.205, R.220 Ligands: ATP.14 19 PLIP interactions: 16 interactions with chain F, 3 interactions with chain E Hydrogen bonds: F:S.137, F:T.157, F:T.157, F:D.159, F:D.159, F:T.175, F:T.181, F:T.181, F:H.201, F:G.202, F:Y.203 Salt bridges: F:K.158, F:K.158, F:R.220, F:R.220, E:K.158, E:K.158, E:K.158 pi-Stacking: F:H.201 ATP.20: 19 residues within 4Å: Chain G: I.154, C.156, T.157, K.158, D.159, T.175, N.179, M.180, T.181, V.182, H.201, G.202, Y.203, L.204, P.205, R.220 Chain H: K.158, R.200 Ligands: ATP.22 20 PLIP interactions: 17 interactions with chain G, 3 interactions with chain H Hydrogen bonds: G:T.157, G:T.157, G:T.157, G:K.158, G:D.159, G:D.159, G:T.175, G:T.181, G:T.181, G:H.201, G:G.202, G:Y.203 Salt bridges: G:K.158, G:R.220, G:R.220, H:K.158, H:K.158, H:K.158 pi-Stacking: G:H.201, G:H.201 ATP.22: 19 residues within 4Å: Chain G: K.158, R.200 Chain H: S.137, I.154, C.156, T.157, K.158, D.159, T.175, N.179, M.180, T.181, H.201, G.202, Y.203, L.204, P.205, R.220 Ligands: ATP.20 19 PLIP interactions: 3 interactions with chain G, 16 interactions with chain H Salt bridges: G:K.158, G:K.158, G:K.158, H:K.158, H:K.158, H:R.220, H:R.220 Hydrogen bonds: H:S.137, H:T.157, H:T.157, H:D.159, H:D.159, H:T.175, H:T.181, H:T.181, H:H.201, H:G.202, H:Y.203 pi-Stacking: H:H.201

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

PO4.3: 7 residues within 4Å: Chain A: S.322, G.360, G.361, L.362, G.382, S.383, M.384 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.361, A:G.382, A:S.383 PO4.6: 6 residues within 4Å: Chain B: G.360, G.361, L.362, R.363, G.382, S.383 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.361, B:L.362, B:G.382, B:S.383 Water bridges: B:S.383, B:M.384 Salt bridges: B:R.363 PO4.9: 7 residues within 4Å: Chain C: S.322, G.360, G.361, L.362, G.382, S.383, M.384 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.361, C:G.382, C:S.383 PO4.12: 6 residues within 4Å: Chain D: G.360, G.361, L.362, R.363, G.382, S.383 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:G.361, D:L.362, D:G.382, D:S.383 Water bridges: D:S.383, D:M.384 Salt bridges: D:R.363 PO4.15: 7 residues within 4Å: Chain E: S.322, G.360, G.361, L.362, G.382, S.383, M.384 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:G.361, E:G.382, E:S.383 PO4.18: 6 residues within 4Å: Chain F: G.360, G.361, L.362, R.363, G.382, S.383 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:G.361, F:L.362, F:G.382, F:S.383 Water bridges: F:S.383, F:M.384 Salt bridges: F:R.363 PO4.21: 7 residues within 4Å: Chain G: S.322, G.360, G.361, L.362, G.382, S.383, M.384 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:G.361, G:G.382, G:S.383 PO4.24: 6 residues within 4Å: Chain H: G.360, G.361, L.362, R.363, G.382, S.383 7 PLIP interactions: 7 interactions with chain H Hydrogen bonds: H:G.361, H:L.362, H:G.382, H:S.383 Water bridges: H:S.383, H:M.384 Salt bridges: H:R.363

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