SMTL ID : 9b14.1

Cryo-EM structure of human uMtCK1 in complex with transition state analog

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-octamer

Ligands

8 x CRN: N-[(E)-AMINO(IMINO)METHYL]-N-METHYLGLYCINE(Non-covalent)

CRN.1: 10 residues within 4Å: Chain A: H.89, I.92, T.94, V.95, L.224, E.255, C.306, S.308, N.309, V.348 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.95 Salt bridges: A:E.255 CRN.4: 10 residues within 4Å: Chain B: H.89, I.92, T.94, V.95, L.224, E.255, C.306, S.308, N.309, V.348 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.95 Salt bridges: B:E.255 CRN.7: 11 residues within 4Å: Chain C: H.89, I.92, T.94, V.95, L.224, E.255, C.306, S.308, N.309, R.343, V.348 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:V.95 Salt bridges: C:E.255 CRN.10: 10 residues within 4Å: Chain D: H.89, I.92, T.94, V.95, L.224, E.255, C.306, S.308, N.309, V.348 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:V.95 Salt bridges: D:E.255 CRN.13: 10 residues within 4Å: Chain E: H.89, I.92, T.94, V.95, L.224, E.255, C.306, S.308, N.309, V.348 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:V.95 Salt bridges: E:E.255 CRN.16: 10 residues within 4Å: Chain F: H.89, I.92, T.94, V.95, L.224, E.255, C.306, S.308, N.309, V.348 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:V.95 Salt bridges: F:E.255 CRN.19: 10 residues within 4Å: Chain G: H.89, I.92, T.94, V.95, L.224, E.255, C.306, S.308, N.309, V.348 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:V.95 Salt bridges: G:E.255 CRN.22: 12 residues within 4Å: Chain H: H.89, I.92, T.94, V.95, S.222, L.224, E.255, C.306, S.308, N.309, R.343, V.348 5 PLIP interactions: 5 interactions with chain H Hydrogen bonds: H:V.95, H:S.308, H:S.308, H:S.308 Salt bridges: H:E.255

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

ADP.2: 20 residues within 4Å: Chain A: S.151, S.152, R.153, R.155, H.214, L.216, F.217, W.251, R.259, M.263, R.315, G.317, V.318, H.319, R.343, G.346, G.347, V.348, D.358 Ligands: MG.3 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:S.151, A:S.151, A:R.153, A:R.315, A:H.319, A:G.346, A:V.348 Salt bridges: A:R.153, A:R.153, A:R.155, A:R.259, A:R.315, A:R.315, A:R.343, A:R.343 pi-Stacking: A:H.319 ADP.5: 20 residues within 4Å: Chain B: S.151, S.152, R.153, R.155, H.214, L.216, F.217, W.251, R.259, M.263, R.315, G.317, V.318, H.319, R.343, G.346, G.347, V.348, D.358 Ligands: MG.6 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:R.153, B:R.315, B:G.317, B:H.319, B:H.319, B:V.348 Salt bridges: B:R.153, B:R.153, B:R.155, B:R.259, B:R.315, B:R.315, B:R.343, B:R.343 pi-Stacking: B:H.319 ADP.8: 19 residues within 4Å: Chain C: S.151, S.152, R.153, R.155, H.214, F.217, W.251, R.259, M.263, R.315, G.317, V.318, H.319, R.343, G.346, G.347, V.348, D.358 Ligands: MG.9 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:S.151, C:S.151, C:R.153, C:R.315, C:H.319, C:G.346, C:V.348 Salt bridges: C:R.153, C:R.155, C:R.259, C:R.315, C:R.315, C:R.343, C:R.343 pi-Stacking: C:H.319 ADP.11: 19 residues within 4Å: Chain D: S.151, S.152, R.153, R.155, H.214, F.217, W.251, R.259, M.263, R.315, G.317, V.318, H.319, R.343, G.346, G.347, V.348, D.358 Ligands: MG.12 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:R.153, D:R.315, D:G.317, D:H.319, D:H.319, D:V.348 Salt bridges: D:R.153, D:R.155, D:R.259, D:R.315, D:R.315, D:R.343, D:R.343 pi-Stacking: D:H.319 ADP.14: 20 residues within 4Å: Chain E: S.151, S.152, R.153, R.155, H.214, L.216, F.217, W.251, R.259, M.263, R.315, G.317, V.318, H.319, R.343, G.346, G.347, V.348, D.358 Ligands: MG.15 15 PLIP interactions: 15 interactions with chain E Hydrogen bonds: E:H.214, E:R.315, E:G.317, E:H.319, E:H.319, E:V.348 Salt bridges: E:R.153, E:R.153, E:R.155, E:R.259, E:R.315, E:R.315, E:R.343, E:R.343 pi-Stacking: E:H.319 ADP.17: 20 residues within 4Å: Chain F: S.151, S.152, R.153, R.155, H.214, L.216, F.217, W.251, R.259, M.263, R.315, G.317, V.318, H.319, R.343, G.346, G.347, V.348, D.358 Ligands: MG.18 13 PLIP interactions: 13 interactions with chain F Hydrogen bonds: F:R.153, F:R.315, F:G.317, F:H.319, F:V.348 Salt bridges: F:R.153, F:R.155, F:R.259, F:R.315, F:R.315, F:R.343, F:R.343 pi-Stacking: F:H.319 ADP.20: 21 residues within 4Å: Chain G: S.151, S.152, R.153, R.155, H.214, L.216, F.217, W.251, R.259, M.263, R.315, G.317, V.318, H.319, R.343, T.345, G.346, G.347, V.348, D.358 Ligands: MG.21 15 PLIP interactions: 15 interactions with chain G Hydrogen bonds: G:R.315, G:G.317, G:H.319, G:T.345, G:G.346, G:V.348 Salt bridges: G:R.153, G:R.153, G:R.155, G:R.259, G:R.315, G:R.315, G:R.343, G:R.343 pi-Stacking: G:H.319 ADP.23: 21 residues within 4Å: Chain H: S.151, S.152, R.153, R.155, H.214, L.216, F.217, W.251, R.259, M.263, R.315, G.317, V.318, H.319, R.343, T.345, G.346, G.347, V.348, D.358 Ligands: MG.24 17 PLIP interactions: 17 interactions with chain H Hydrogen bonds: H:R.153, H:H.214, H:R.315, H:G.317, H:H.319, H:T.345, H:G.346, H:V.348 Salt bridges: H:R.153, H:R.153, H:R.155, H:R.259, H:R.315, H:R.315, H:R.343, H:R.343 pi-Stacking: H:H.319

8 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.3: 4 residues within 4Å: Chain A: W.251, E.254, R.259 Ligands: ADP.2 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain B: E.254 Ligands: ADP.5 No protein-ligand interaction detected (PLIP) MG.9: 3 residues within 4Å: Chain C: W.251, R.259 Ligands: ADP.8 No protein-ligand interaction detected (PLIP) MG.12: 2 residues within 4Å: Chain D: E.254 Ligands: ADP.11 No protein-ligand interaction detected (PLIP) MG.15: 2 residues within 4Å: Chain E: E.254 Ligands: ADP.14 No protein-ligand interaction detected (PLIP) MG.18: 2 residues within 4Å: Chain F: E.254 Ligands: ADP.17 No protein-ligand interaction detected (PLIP) MG.21: 2 residues within 4Å: Chain G: E.254 Ligands: ADP.20 No protein-ligand interaction detected (PLIP) MG.24: 2 residues within 4Å: Chain H: E.254 Ligands: ADP.23 No protein-ligand interaction detected (PLIP)

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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