SMTL ID : 9b0t.1

Cryo-EM structure of E227Q variant of 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: T.94, V.95, R.119, L.225, M.230, C.306, S.308, R.343, V.348 Ligands: NO3.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.95 CRN.5: 10 residues within 4Å: Chain B: T.94, V.95, R.119, L.225, M.230, C.306, S.308, R.343, V.348 Ligands: NO3.7 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.95 CRN.9: 10 residues within 4Å: Chain C: T.94, V.95, R.119, L.225, M.230, C.306, S.308, R.343, V.348 Ligands: NO3.11 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:V.95 CRN.13: 10 residues within 4Å: Chain D: T.94, V.95, R.119, L.225, M.230, C.306, S.308, R.343, V.348 Ligands: NO3.15 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:V.95 CRN.17: 10 residues within 4Å: Chain E: T.94, V.95, R.119, L.225, M.230, C.306, S.308, R.343, V.348 Ligands: NO3.19 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:V.95 CRN.21: 10 residues within 4Å: Chain F: T.94, V.95, R.119, L.225, M.230, C.306, S.308, R.343, V.348 Ligands: NO3.23 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:V.95 CRN.25: 10 residues within 4Å: Chain G: T.94, V.95, R.119, L.225, M.230, C.306, S.308, R.343, V.348 Ligands: NO3.27 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:V.95 CRN.29: 10 residues within 4Å: Chain H: T.94, V.95, R.119, L.225, M.230, C.306, S.308, R.343, V.348 Ligands: NO3.31 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:V.95

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

ADP.2: 19 residues within 4Å: Chain A: S.151, S.152, R.153, R.155, I.211, H.214, W.251, R.259, R.315, G.317, V.318, H.319, R.343, G.346, G.347, V.348, D.358 Ligands: NO3.3, MG.4 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:S.151, A:S.151, A:H.214, A:R.315, A:H.319, 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.6: 20 residues within 4Å: Chain B: S.151, R.153, R.155, I.211, H.214, L.216, F.217, W.251, R.259, R.315, G.317, V.318, H.319, R.343, G.346, G.347, V.348, D.358 Ligands: NO3.7, MG.8 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:S.151, B:S.151, B:R.153, B:I.211, B:R.315, 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.10: 20 residues within 4Å: Chain C: S.151, R.153, R.155, I.211, H.214, L.216, F.217, W.251, R.259, R.315, G.317, V.318, H.319, R.343, G.346, G.347, V.348, D.358 Ligands: NO3.11, MG.12 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:S.151, C:S.151, C:R.153, C:R.315, C:V.348 Salt bridges: C:R.153, 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.14: 19 residues within 4Å: Chain D: S.151, S.152, R.153, R.155, I.211, H.214, W.251, R.259, R.315, G.317, V.318, H.319, R.343, G.346, G.347, V.348, D.358 Ligands: NO3.15, MG.16 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:S.151, D:S.151, D:H.214, D:R.315, D:H.319, D:V.348 Salt bridges: D:R.153, 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.18: 19 residues within 4Å: Chain E: S.151, R.153, R.155, I.211, H.214, L.216, W.251, R.259, R.315, G.317, V.318, H.319, R.343, G.346, G.347, V.348, D.358 Ligands: NO3.19, MG.20 15 PLIP interactions: 15 interactions with chain E Hydrogen bonds: E:S.151, E:S.151, E:R.153, E:R.315, 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.22: 19 residues within 4Å: Chain F: S.151, R.153, R.155, I.211, H.214, L.216, W.251, R.259, R.315, G.317, V.318, H.319, R.343, G.346, G.347, V.348, D.358 Ligands: NO3.23, MG.24 15 PLIP interactions: 15 interactions with chain F Hydrogen bonds: F:S.151, F:S.151, F:R.153, F:R.315, F:H.319, F:V.348 Salt bridges: F:R.153, 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.26: 20 residues within 4Å: Chain G: S.151, R.153, R.155, I.211, H.214, L.216, F.217, W.251, R.259, R.315, G.317, V.318, H.319, R.343, G.346, G.347, V.348, D.358 Ligands: NO3.27, MG.28 15 PLIP interactions: 15 interactions with chain G Hydrogen bonds: G:S.151, G:S.151, G:R.153, G:R.315, G:H.319, 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.30: 19 residues within 4Å: Chain H: S.151, R.153, R.155, I.211, H.214, L.216, W.251, R.259, R.315, G.317, V.318, H.319, R.343, G.346, G.347, V.348, D.358 Ligands: NO3.31, MG.32 15 PLIP interactions: 15 interactions with chain H Hydrogen bonds: H:S.151, H:S.151, H:R.153, H:R.315, H:H.319, 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 NO3: NITRATE ION(Non-functional Binders)

NO3.3: 11 residues within 4Å: Chain A: R.155, Q.255, R.259, N.309, R.315, R.343, V.348, R.364 Ligands: CRN.1, ADP.2, MG.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.259, A:N.309, A:R.343, A:R.343, A:R.364 NO3.7: 11 residues within 4Å: Chain B: R.155, Q.255, R.259, N.309, R.315, R.343, V.348, R.364 Ligands: CRN.5, ADP.6, MG.8 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.259, B:N.309, B:R.343, B:R.343, B:R.364 NO3.11: 11 residues within 4Å: Chain C: R.155, Q.255, R.259, N.309, R.315, R.343, V.348, R.364 Ligands: CRN.9, ADP.10, MG.12 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.259, C:N.309, C:R.343, C:R.343, C:R.364 NO3.15: 11 residues within 4Å: Chain D: R.155, Q.255, R.259, N.309, R.315, R.343, V.348, R.364 Ligands: CRN.13, ADP.14, MG.16 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:R.259, D:N.309, D:R.343, D:R.343, D:R.364 NO3.19: 11 residues within 4Å: Chain E: R.155, Q.255, R.259, N.309, R.315, R.343, V.348, R.364 Ligands: CRN.17, ADP.18, MG.20 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:R.259, E:N.309, E:R.343, E:R.343, E:R.364 NO3.23: 11 residues within 4Å: Chain F: R.155, Q.255, R.259, N.309, R.315, R.343, V.348, R.364 Ligands: CRN.21, ADP.22, MG.24 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:R.259, F:N.309, F:R.343, F:R.343, F:R.364 NO3.27: 11 residues within 4Å: Chain G: R.155, Q.255, R.259, N.309, R.315, R.343, V.348, R.364 Ligands: CRN.25, ADP.26, MG.28 5 PLIP interactions: 5 interactions with chain G Hydrogen bonds: G:R.259, G:N.309, G:R.343, G:R.343, G:R.364 NO3.31: 11 residues within 4Å: Chain H: R.155, Q.255, R.259, N.309, R.315, R.343, V.348, R.364 Ligands: CRN.29, ADP.30, MG.32 5 PLIP interactions: 5 interactions with chain H Hydrogen bonds: H:R.259, H:N.309, H:R.343, H:R.343, H:R.364

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

MG.4: 4 residues within 4Å: Chain A: W.251, R.259 Ligands: ADP.2, NO3.3 No protein-ligand interaction detected (PLIP) MG.8: 4 residues within 4Å: Chain B: W.251, R.259 Ligands: ADP.6, NO3.7 No protein-ligand interaction detected (PLIP) MG.12: 4 residues within 4Å: Chain C: W.251, R.259 Ligands: ADP.10, NO3.11 No protein-ligand interaction detected (PLIP) MG.16: 4 residues within 4Å: Chain D: W.251, R.259 Ligands: ADP.14, NO3.15 No protein-ligand interaction detected (PLIP) MG.20: 4 residues within 4Å: Chain E: W.251, R.259 Ligands: ADP.18, NO3.19 No protein-ligand interaction detected (PLIP) MG.24: 4 residues within 4Å: Chain F: W.251, R.259 Ligands: ADP.22, NO3.23 No protein-ligand interaction detected (PLIP) MG.28: 4 residues within 4Å: Chain G: W.251, R.259 Ligands: ADP.26, NO3.27 No protein-ligand interaction detected (PLIP) MG.32: 4 residues within 4Å: Chain H: W.251, R.259 Ligands: ADP.30, NO3.31 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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