SMTL ID : 9b0u.1

Cryo-EM structure of E227Q variant of uMtCK1 incubated with ADP and phosphocreatine at pH 8.0

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: 11 residues within 4Å: Chain A: H.89, I.92, T.94, V.95, L.224, L.225, Q.255, C.306, S.308, V.348 Ligands: PO4.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.95, A:Q.255 CRN.5: 11 residues within 4Å: Chain B: H.89, I.92, T.94, V.95, L.224, L.225, Q.255, C.306, S.308, V.348 Ligands: PO4.7 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.95, B:Q.255 CRN.11: 11 residues within 4Å: Chain C: H.89, I.92, T.94, V.95, L.224, L.225, Q.255, C.306, S.308, V.348 Ligands: PO4.10 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:V.95, C:Q.255 CRN.13: 11 residues within 4Å: Chain D: H.89, I.92, T.94, V.95, L.224, L.225, Q.255, C.306, S.308, V.348 Ligands: PO4.15 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:V.95, D:Q.255 CRN.17: 11 residues within 4Å: Chain E: H.89, I.92, T.94, V.95, L.224, L.225, Q.255, C.306, S.308, V.348 Ligands: PO4.19 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:V.95, E:Q.255 CRN.21: 11 residues within 4Å: Chain F: H.89, I.92, T.94, V.95, L.224, L.225, Q.255, C.306, S.308, V.348 Ligands: PO4.23 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:V.95, F:Q.255 CRN.25: 11 residues within 4Å: Chain G: H.89, I.92, T.94, V.95, L.224, L.225, Q.255, C.306, S.308, V.348 Ligands: PO4.27 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:V.95, G:Q.255 CRN.29: 11 residues within 4Å: Chain H: H.89, I.92, T.94, V.95, L.224, L.225, Q.255, C.306, S.308, V.348 Ligands: PO4.31 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:V.95, H:Q.255

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

ADP.2: 19 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, R.343, G.346, G.347, V.348, D.358 Ligands: PO4.3, MG.4 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:S.151, A:S.151, A:R.315, A:H.319, A:H.319, A:G.347, 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, S.152, R.153, R.155, H.214, 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: PO4.7, MG.8 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:R.153, B:R.315, B:G.317, B:H.319, B:T.345, B:G.346, 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.9: 19 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, G.347, V.348, D.358 Ligands: PO4.10, MG.12 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:S.151, C:R.153, C:R.315, C:G.317, C:H.319, C:G.347, 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, H.214, 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: PO4.15, MG.16 16 PLIP interactions: 16 interactions with chain D Hydrogen bonds: D:S.151, D:S.151, D:R.315, D:H.319, D:H.319, D:G.347, 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: 21 residues within 4Å: Chain E: S.151, S.152, R.153, R.155, H.214, L.216, 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: PO4.19, MG.20 17 PLIP interactions: 17 interactions with chain E Hydrogen bonds: E:R.153, E:R.315, E:G.317, E:H.319, E:H.319, E:G.346, E:G.346, 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, 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, G.347, V.348, D.358 Ligands: PO4.23, MG.24 16 PLIP interactions: 16 interactions with chain F Hydrogen bonds: F:S.151, F:S.151, F:R.315, F:H.319, F:H.319, F:G.347, 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: 19 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, G.347, V.348, D.358 Ligands: PO4.27, MG.28 17 PLIP interactions: 17 interactions with chain G Hydrogen bonds: G:S.151, G:S.151, G:R.153, G:R.315, G:H.319, G:H.319, G:G.347, 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: 20 residues within 4Å: Chain H: S.151, S.152, R.153, R.155, H.214, L.216, 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: PO4.31, MG.32 14 PLIP interactions: 14 interactions with chain H Hydrogen bonds: H:S.151, H:S.151, 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 PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 9 residues within 4Å: Chain A: R.155, Q.255, R.259, N.309, R.343, V.348 Ligands: CRN.1, ADP.2, MG.4 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.255, A:N.309, A:N.309 Salt bridges: A:R.155, A:R.259, A:R.343 PO4.7: 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:Q.255, B:N.309 Salt bridges: B:R.155, B:R.259, B:R.343 PO4.10: 9 residues within 4Å: Chain C: R.155, Q.255, R.259, N.309, R.343, V.348 Ligands: ADP.9, CRN.11, MG.12 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Q.255, C:N.309 Salt bridges: C:R.155, C:R.259, C:R.343 PO4.15: 10 residues within 4Å: Chain D: R.155, Q.255, R.259, N.309, R.343, V.348, R.364 Ligands: CRN.13, ADP.14, MG.16 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:Q.255, D:N.309, D:N.309 Salt bridges: D:R.155, D:R.259, D:R.343 PO4.19: 8 residues within 4Å: Chain E: R.155, Q.255, R.259, N.309, R.343 Ligands: CRN.17, ADP.18, MG.20 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:Q.255, E:N.309, E:N.309 Salt bridges: E:R.155, E:R.259, E:R.343 PO4.23: 10 residues within 4Å: Chain F: R.155, Q.255, R.259, N.309, R.315, R.343, R.364 Ligands: CRN.21, ADP.22, MG.24 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:Q.255, F:N.309 Salt bridges: F:R.155, F:R.259, F:R.343 PO4.27: 10 residues within 4Å: Chain G: R.155, Q.255, R.259, N.309, R.343, V.348, R.364 Ligands: CRN.25, ADP.26, MG.28 5 PLIP interactions: 5 interactions with chain G Hydrogen bonds: G:Q.255, G:N.309 Salt bridges: G:R.155, G:R.259, G:R.343 PO4.31: 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:Q.255, H:N.309 Salt bridges: H:R.155, H:R.259, H:R.343

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

MG.4: 4 residues within 4Å: Chain A: R.259, R.343 Ligands: ADP.2, PO4.3 No protein-ligand interaction detected (PLIP) MG.8: 4 residues within 4Å: Chain B: Q.255, R.259 Ligands: ADP.6, PO4.7 No protein-ligand interaction detected (PLIP) MG.12: 5 residues within 4Å: Chain C: Q.255, R.259, R.343 Ligands: ADP.9, PO4.10 No protein-ligand interaction detected (PLIP) MG.16: 4 residues within 4Å: Chain D: Q.255, R.259 Ligands: ADP.14, PO4.15 No protein-ligand interaction detected (PLIP) MG.20: 5 residues within 4Å: Chain E: Q.255, R.259, R.343 Ligands: ADP.18, PO4.19 No protein-ligand interaction detected (PLIP) MG.24: 4 residues within 4Å: Chain F: R.259, R.343 Ligands: ADP.22, PO4.23 No protein-ligand interaction detected (PLIP) MG.28: 4 residues within 4Å: Chain G: R.259, R.343 Ligands: ADP.26, PO4.27 No protein-ligand interaction detected (PLIP) MG.32: 4 residues within 4Å: Chain H: Q.255, R.259 Ligands: ADP.30, PO4.31 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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