SMTL ID : 9exo.1

Wzc-K540M-2YE MgADP C1

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: P.473, S.475, P.536, S.537, A.538, G.539, M.540, T.541, F.542, Y.569, R.667, N.696 Ligands: MG.2 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:P.473, A:S.475, A:S.537, A:A.538, A:G.539, A:M.540, A:T.541, A:F.542, A:R.667 pi-Stacking: A:F.542, A:F.542 ADP.3: 13 residues within 4Å: Chain B: P.473, I.474, S.475, P.536, S.537, A.538, G.539, M.540, T.541, F.542, Y.569, N.696 Ligands: MG.4 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:P.473, B:S.475, B:S.537, B:A.538, B:G.539, B:M.540, B:T.541, B:F.542, B:N.696 pi-Stacking: B:F.542, B:F.542 pi-Cation interactions: B:R.667 ADP.5: 13 residues within 4Å: Chain C: P.473, S.475, P.536, S.537, A.538, G.539, M.540, T.541, F.542, Y.569, R.667, N.696 Ligands: MG.6 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:P.473, C:S.475, C:S.537, C:A.538, C:G.539, C:M.540, C:T.541, C:F.542, C:R.667, C:N.696 pi-Stacking: C:F.542, C:F.542 pi-Cation interactions: C:R.667 ADP.7: 14 residues within 4Å: Chain D: P.473, I.474, S.475, P.536, S.537, A.538, G.539, M.540, T.541, F.542, Y.569, R.667, N.696 Ligands: MG.8 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:P.473, D:S.475, D:S.537, D:A.538, D:G.539, D:M.540, D:T.541, D:F.542, D:R.667, D:N.696 pi-Stacking: D:F.542, D:F.542 ADP.9: 14 residues within 4Å: Chain E: I.472, P.473, I.474, S.475, P.536, S.537, A.538, G.539, M.540, T.541, F.542, Y.569, N.696 Ligands: MG.10 12 PLIP interactions: 12 interactions with chain E Hydrogen bonds: E:P.473, E:S.475, E:S.537, E:A.538, E:G.539, E:M.540, E:T.541, E:F.542, E:N.696 pi-Stacking: E:F.542, E:F.542 pi-Cation interactions: E:R.667 ADP.11: 14 residues within 4Å: Chain F: P.473, I.474, S.475, P.536, S.537, A.538, G.539, M.540, T.541, F.542, Y.569, R.667, N.696 Ligands: MG.12 13 PLIP interactions: 13 interactions with chain F Hydrogen bonds: F:P.473, F:S.475, F:S.537, F:A.538, F:G.539, F:M.540, F:T.541, F:F.542, F:R.667, F:N.696 pi-Stacking: F:F.542, F:F.542 pi-Cation interactions: F:R.667 ADP.13: 14 residues within 4Å: Chain G: P.473, I.474, S.475, P.536, S.537, A.538, G.539, M.540, T.541, F.542, Y.569, R.667, N.696 Ligands: MG.14 16 PLIP interactions: 16 interactions with chain G Hydrogen bonds: G:P.473, G:S.475, G:S.537, G:A.538, G:G.539, G:M.540, G:T.541, G:T.541, G:F.542, G:Y.569, G:R.667, G:N.696, G:G.697 pi-Stacking: G:F.542, G:F.542 pi-Cation interactions: G:R.667 ADP.15: 13 residues within 4Å: Chain H: P.473, S.475, P.536, S.537, A.538, G.539, M.540, T.541, F.542, Y.569, R.667, N.696 Ligands: MG.16 13 PLIP interactions: 13 interactions with chain H Hydrogen bonds: H:S.475, H:S.537, H:A.538, H:G.539, H:M.540, H:T.541, H:F.542, H:Y.569, H:R.667, H:N.696, H:G.697 pi-Stacking: H:F.542, H:F.542

8 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: T.541, D.564, D.642 Ligands: ADP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.541 MG.4: 4 residues within 4Å: Chain B: T.541, D.564, D.642 Ligands: ADP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.541 MG.6: 4 residues within 4Å: Chain C: T.541, D.564, D.642 Ligands: ADP.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.541 MG.8: 4 residues within 4Å: Chain D: T.541, D.564, D.642 Ligands: ADP.7 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.541 MG.10: 4 residues within 4Å: Chain E: T.541, D.564, D.642 Ligands: ADP.9 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.541 MG.12: 4 residues within 4Å: Chain F: T.541, D.564, D.642 Ligands: ADP.11 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.541 MG.14: 4 residues within 4Å: Chain G: T.541, D.564, D.642 Ligands: ADP.13 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:T.541 MG.16: 4 residues within 4Å: Chain H: T.541, D.564, D.642 Ligands: ADP.15 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:T.541

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, Y. et al., Molecular basis for the phosphorylation of bacterial tyrosine kinase Wzc. Nat Commun (2025)

Release Date

2025-04-23

Peptides

Putative transmembrane protein Wzc: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
A

C
B

D
C

E
D

F
E

G
F

H
G

Membrane

We predict this structure to be a membrane protein.
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Putative transmembrane protein Wzc

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