SMTL ID : 9b16.1

Cryo-EM structure of human uMtCK1 in complex with ADP and covalent inhibitor CKi

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-octamer

Ligands

8 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 13 residues within 4Å: Chain A: S.151, S.152, R.153, R.155, H.214, W.251, R.259, M.263, R.315, G.317, V.318, H.319, G.346 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:S.151, A:S.151, A:H.319, A:G.346 Salt bridges: A:R.153, A:R.153, A:R.155, A:R.315, A:R.315 pi-Stacking: A:H.319 ADP.3: 15 residues within 4Å: Chain B: S.151, S.152, R.153, R.155, H.214, W.251, R.259, M.263, R.315, G.317, V.318, H.319, R.343, G.346, D.358 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:S.151, B:S.151, B:H.319, B:G.346 Salt bridges: B:R.153, B:R.153, B:R.155, B:R.315, B:R.315 pi-Stacking: B:H.319 ADP.5: 15 residues within 4Å: Chain C: S.151, S.152, R.153, R.155, H.214, W.251, R.259, M.263, R.315, G.317, V.318, H.319, R.343, G.346, D.358 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:S.151, C:S.151, C:H.319, C:G.346 Salt bridges: C:R.153, C:R.153, C:R.155, C:R.315, C:R.315 pi-Stacking: C:H.319 ADP.7: 14 residues within 4Å: Chain D: S.151, S.152, R.153, R.155, H.214, W.251, R.259, M.263, R.315, G.317, V.318, H.319, R.343, G.346 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:S.151, D:S.151, D:H.319, D:G.346 Salt bridges: D:R.153, D:R.153, D:R.155, D:R.315, D:R.315 pi-Stacking: D:H.319 ADP.9: 13 residues within 4Å: Chain E: S.151, S.152, R.153, R.155, H.214, W.251, R.259, M.263, R.315, G.317, V.318, H.319, G.346 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:S.151, E:S.151, E:H.319, E:G.346 Salt bridges: E:R.153, E:R.153, E:R.155, E:R.315, E:R.315 pi-Stacking: E:H.319 ADP.11: 13 residues within 4Å: Chain F: S.151, S.152, R.153, R.155, H.214, W.251, R.259, M.263, R.315, G.317, V.318, H.319, G.346 10 PLIP interactions: 10 interactions with chain F Hydrogen bonds: F:S.151, F:S.151, F:H.319, F:G.346 Salt bridges: F:R.153, F:R.153, F:R.155, F:R.315, F:R.315 pi-Stacking: F:H.319 ADP.13: 15 residues within 4Å: Chain G: S.151, S.152, R.153, R.155, H.214, W.251, R.259, M.263, R.315, G.317, V.318, H.319, R.343, G.346, D.358 10 PLIP interactions: 10 interactions with chain G Hydrogen bonds: G:S.151, G:S.151, G:H.319, G:G.346 Salt bridges: G:R.153, G:R.153, G:R.155, G:R.315, G:R.315 pi-Stacking: G:H.319 ADP.15: 14 residues within 4Å: Chain H: S.151, S.152, R.153, R.155, H.214, W.251, R.259, M.263, R.315, G.317, V.318, H.319, R.343, G.346 11 PLIP interactions: 11 interactions with chain H Hydrogen bonds: H:S.151, H:S.151, H:H.319, H:G.346 Salt bridges: H:R.153, H:R.153, H:R.155, H:R.315, H:R.315, H:R.343 pi-Stacking: H:H.319

8 x KLU: (2S)-4-(chloroacetyl)-3,4-dihydro-2H-1,4-benzoxazine-2-carboxamide(Covalent)

KLU.2: 13 residues within 4Å: Chain A: T.82, T.94, V.95, G.96, M.97, V.98, L.224, L.225, A.228, M.230, E.255, C.306, S.308 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.224, A:L.225, A:A.228 Hydrogen bonds: A:T.82, A:G.96, A:G.96 KLU.4: 12 residues within 4Å: Chain B: T.82, T.94, V.95, G.96, M.97, L.224, L.225, A.228, M.230, E.255, C.306, S.308 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.225, B:L.225, B:A.228, B:E.255 Hydrogen bonds: B:T.82, B:G.96, B:M.97 KLU.6: 12 residues within 4Å: Chain C: T.82, T.94, V.95, G.96, M.97, L.224, L.225, A.228, M.230, E.255, C.306, S.308 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:L.225, C:L.225, C:A.228 Hydrogen bonds: C:T.82, C:G.96, C:G.96 KLU.8: 12 residues within 4Å: Chain D: T.82, T.94, V.95, G.96, M.97, L.224, L.225, A.228, M.230, E.255, C.306, S.308 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:L.224, D:L.225, D:L.225, D:A.228 Hydrogen bonds: D:G.96, D:G.96 KLU.10: 13 residues within 4Å: Chain E: T.82, T.94, V.95, G.96, M.97, V.98, L.224, L.225, A.228, M.230, E.255, C.306, S.308 6 PLIP interactions: 6 interactions with chain E Hydrophobic interactions: E:L.225, E:L.225, E:A.228 Hydrogen bonds: E:T.82, E:T.82, E:G.96 KLU.12: 13 residues within 4Å: Chain F: T.82, T.94, V.95, G.96, M.97, V.98, L.224, L.225, A.228, M.230, E.255, C.306, S.308 6 PLIP interactions: 6 interactions with chain F Hydrophobic interactions: F:L.224, F:L.225, F:A.228 Hydrogen bonds: F:T.82, F:G.96, F:M.97 KLU.14: 12 residues within 4Å: Chain G: T.82, T.94, V.95, G.96, M.97, L.224, L.225, A.228, M.230, E.255, C.306, S.308 6 PLIP interactions: 6 interactions with chain G Hydrophobic interactions: G:L.225, G:L.225, G:A.228 Hydrogen bonds: G:T.82, G:G.96, G:G.96 KLU.16: 13 residues within 4Å: Chain H: T.82, T.94, V.95, G.96, M.97, V.98, L.224, L.225, A.228, M.230, E.255, C.306, S.308 7 PLIP interactions: 7 interactions with chain H Hydrophobic interactions: H:L.224, H:L.225, H:A.228 Hydrogen bonds: H:T.82, H:T.82, H:V.95, H:G.96

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Demir, M. et al., Structural basis for substrate binding, catalysis and inhibition of cancer target mitochondrial creatine kinase by a covalent inhibitor. Structure (2025)

Release Date

2025-02-12

Peptides

Creatine kinase U-type, mitochondrial: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

Creatine kinase U-type, mitochondrial

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