SMTL ID : 6rfu.1

In cellulo crystallization of Trypanosoma brucei IMP dehydrogenase enables the identification of ATP and GMP as genuine co-factors

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-octamer

Ligands

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

ATP.1: 22 residues within 4Å: Chain A: K.130, S.136, G.137, 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 16 PLIP interactions: 14 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.136, A:T.156, A:K.157, A:D.158, A:D.158, A:T.180, A:T.180, A:G.201 Salt bridges: A:K.130, A:K.157, A:K.157, A:R.219, B:K.157, B:K.157 pi-Stacking: A:H.200, A:H.200 ATP.3: 20 residues within 4Å: Chain A: K.157, R.199 Chain B: S.136, G.137, I.153, C.155, T.156, K.157, D.158, T.174, N.178, M.179, T.180, V.181, H.200, G.201, Y.202, L.203, P.204, R.219 15 PLIP interactions: 13 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.136, B:S.136, B:T.156, B:T.156, B:D.158, B:D.158, B:T.180, B:T.180, B:G.201 Salt bridges: B:K.157, B:R.219, A:K.157, A:K.157 pi-Stacking: B:H.200, B:H.200 ATP.5: 22 residues within 4Å: Chain C: K.130, S.136, G.137, 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 16 PLIP interactions: 14 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:S.136, C:T.156, C:K.157, C:D.158, C:D.158, C:T.180, C:T.180, C:G.201 Salt bridges: C:K.130, C:K.157, C:K.157, C:R.219, D:K.157, D:K.157 pi-Stacking: C:H.200, C:H.200 ATP.7: 20 residues within 4Å: Chain C: K.157, R.199 Chain D: S.136, G.137, I.153, C.155, T.156, K.157, D.158, T.174, N.178, M.179, T.180, V.181, H.200, G.201, Y.202, L.203, P.204, R.219 15 PLIP interactions: 13 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:S.136, D:S.136, D:T.156, D:T.156, D:D.158, D:D.158, D:T.180, D:T.180, D:G.201 Salt bridges: D:K.157, D:R.219, C:K.157, C:K.157 pi-Stacking: D:H.200, D:H.200 ATP.9: 22 residues within 4Å: Chain E: K.130, S.136, G.137, 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 16 PLIP interactions: 14 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:S.136, E:T.156, E:K.157, E:D.158, E:D.158, E:T.180, E:T.180, E:G.201 Salt bridges: E:K.130, E:K.157, E:K.157, E:R.219, F:K.157, F:K.157 pi-Stacking: E:H.200, E:H.200 ATP.11: 20 residues within 4Å: Chain E: K.157, R.199 Chain F: S.136, G.137, I.153, C.155, T.156, K.157, D.158, T.174, N.178, M.179, T.180, V.181, H.200, G.201, Y.202, L.203, P.204, R.219 15 PLIP interactions: 13 interactions with chain F, 2 interactions with chain E Hydrogen bonds: F:S.136, F:S.136, F:T.156, F:T.156, F:D.158, F:D.158, F:T.180, F:T.180, F:G.201 Salt bridges: F:K.157, F:R.219, E:K.157, E:K.157 pi-Stacking: F:H.200, F:H.200 ATP.13: 22 residues within 4Å: Chain G: K.130, S.136, G.137, 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 16 PLIP interactions: 14 interactions with chain G, 2 interactions with chain H Hydrogen bonds: G:S.136, G:T.156, G:K.157, G:D.158, G:D.158, G:T.180, G:T.180, G:G.201 Salt bridges: G:K.130, G:K.157, G:K.157, G:R.219, H:K.157, H:K.157 pi-Stacking: G:H.200, G:H.200 ATP.15: 20 residues within 4Å: Chain G: K.157, R.199 Chain H: S.136, G.137, I.153, C.155, T.156, K.157, D.158, T.174, N.178, M.179, T.180, V.181, H.200, G.201, Y.202, L.203, P.204, R.219 15 PLIP interactions: 13 interactions with chain H, 2 interactions with chain G Hydrogen bonds: H:S.136, H:S.136, H:T.156, H:T.156, H:D.158, H:D.158, H:T.180, H:T.180, H:G.201 Salt bridges: H:K.157, H:R.219, G:K.157, G:K.157 pi-Stacking: H:H.200, H:H.200

8 x 5GP: GUANOSINE-5'-MONOPHOSPHATE(Non-covalent)

5GP.2: 16 residues within 4Å: Chain A: L.105, N.108, I.111, M.112, K.113, P.114, K.115, K.133, I.135, S.136, G.137, I.138, L.139, Y.202, L.215, S.217 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:M.112, A:K.115, A:S.136, A:G.137, A:S.217 Salt bridges: A:K.115, A:K.133 5GP.4: 15 residues within 4Å: Chain B: 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 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.115, B:S.136, B:G.137 Salt bridges: B:K.115, B:K.133 5GP.6: 16 residues within 4Å: Chain C: L.105, N.108, I.111, M.112, K.113, P.114, K.115, K.133, I.135, S.136, G.137, I.138, L.139, Y.202, L.215, S.217 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:M.112, C:K.115, C:S.136, C:G.137, C:S.217 Salt bridges: C:K.115, C:K.133 5GP.8: 15 residues within 4Å: Chain D: 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 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:K.115, D:S.136, D:G.137 Salt bridges: D:K.115, D:K.133 5GP.10: 16 residues within 4Å: Chain E: L.105, N.108, I.111, M.112, K.113, P.114, K.115, K.133, I.135, S.136, G.137, I.138, L.139, Y.202, L.215, S.217 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:M.112, E:K.115, E:S.136, E:G.137, E:S.217 Salt bridges: E:K.115, E:K.133 5GP.12: 15 residues within 4Å: Chain F: 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 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:K.115, F:S.136, F:G.137 Salt bridges: F:K.115, F:K.133 5GP.14: 16 residues within 4Å: Chain G: L.105, N.108, I.111, M.112, K.113, P.114, K.115, K.133, I.135, S.136, G.137, I.138, L.139, Y.202, L.215, S.217 7 PLIP interactions: 7 interactions with chain G Hydrogen bonds: G:M.112, G:K.115, G:S.136, G:G.137, G:S.217 Salt bridges: G:K.115, G:K.133 5GP.16: 15 residues within 4Å: Chain H: 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 5 PLIP interactions: 5 interactions with chain H Hydrogen bonds: H:K.115, H:S.136, H:G.137 Salt bridges: H:K.115, H:K.133

Links

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Citation

Nass, K. et al., In cellulo crystallization of Trypanosoma brucei IMP dehydrogenase enables the identification of genuine co-factors. Nat Commun (2020)

Release Date

2020-02-19

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