SMTL ID : 3la6.2 (1 other biounit)

Octameric kinase domain of the E. coli tyrosine kinase Wzc with bound ADP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

homo-octamer

Ligands

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

ADP.1: 18 residues within 4Å: Chain A: I.36, P.37, L.38, S.39, Q.42, D.46, K.58, Q.59, S.103, I.104, G.105, M.106, T.107, F.108, Y.135, N.262, S.263 Ligands: CA.2 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:S.39, A:K.58, A:K.58, A:Q.59, A:Q.59, A:S.103, A:I.104, A:G.105, A:M.106, A:T.107, A:T.107, A:F.108, A:N.262, A:N.262, A:S.263 pi-Stacking: A:F.108, A:F.108 ADP.3: 18 residues within 4Å: Chain B: I.36, P.37, L.38, S.39, Q.42, D.46, K.58, Q.59, S.103, I.104, G.105, M.106, T.107, F.108, Y.135, N.262, S.263 Ligands: CA.4 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:P.37, B:S.39, B:K.58, B:K.58, B:Q.59, B:Q.59, B:S.103, B:I.104, B:G.105, B:M.106, B:T.107, B:T.107, B:F.108, B:N.262, B:S.263 pi-Stacking: B:F.108, B:F.108 ADP.5: 18 residues within 4Å: Chain C: I.36, P.37, L.38, S.39, Q.42, D.46, K.58, Q.59, S.103, I.104, G.105, M.106, T.107, F.108, Y.135, N.262, S.263 Ligands: CA.6 17 PLIP interactions: 17 interactions with chain C Hydrogen bonds: C:S.39, C:K.58, C:K.58, C:Q.59, C:Q.59, C:S.103, C:I.104, C:G.105, C:M.106, C:T.107, C:T.107, C:F.108, C:N.262, C:N.262, C:S.263 pi-Stacking: C:F.108, C:F.108 ADP.7: 16 residues within 4Å: Chain D: I.36, P.37, L.38, S.39, Q.42, D.46, S.103, I.104, G.105, M.106, T.107, F.108, Y.135, N.262, S.263 Ligands: CA.8 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:S.39, D:S.103, D:I.104, D:G.105, D:M.106, D:T.107, D:T.107, D:F.108, D:Y.135, D:N.262, D:N.262, D:S.263 pi-Stacking: D:F.108, D:F.108 ADP.9: 16 residues within 4Å: Chain E: I.36, P.37, L.38, S.39, Q.42, D.46, S.103, I.104, G.105, M.106, T.107, F.108, Y.135, N.262, S.263 Ligands: CA.10 14 PLIP interactions: 14 interactions with chain E Hydrogen bonds: E:P.37, E:S.39, E:S.103, E:I.104, E:G.105, E:M.106, E:T.107, E:T.107, E:F.108, E:Y.135, E:N.262, E:S.263 pi-Stacking: E:F.108, E:F.108 ADP.11: 20 residues within 4Å: Chain F: I.36, P.37, L.38, S.39, Q.42, D.46, K.58, Q.59, S.101, P.102, S.103, I.104, G.105, M.106, T.107, F.108, Y.135, N.262, S.263 Ligands: CA.12 19 PLIP interactions: 19 interactions with chain F Hydrogen bonds: F:P.37, F:S.39, F:K.58, F:K.58, F:Q.59, F:Q.59, F:S.101, F:S.103, F:I.104, F:G.105, F:G.105, F:M.106, F:T.107, F:F.108, F:Y.135, F:N.262, F:S.263 pi-Stacking: F:F.108, F:F.108 ADP.13: 17 residues within 4Å: Chain G: I.36, P.37, L.38, S.39, Q.42, D.46, Q.59, S.103, I.104, G.105, M.106, T.107, F.108, Y.135, N.262, S.263 Ligands: CA.14 16 PLIP interactions: 16 interactions with chain G Hydrogen bonds: G:S.39, G:Q.59, G:Q.59, G:S.103, G:I.104, G:G.105, G:M.106, G:T.107, G:T.107, G:F.108, G:Y.135, G:N.262, G:N.262, G:S.263 pi-Stacking: G:F.108, G:F.108 ADP.15: 16 residues within 4Å: Chain H: I.36, P.37, L.38, S.39, Q.42, D.46, S.103, I.104, G.105, M.106, T.107, F.108, Y.135, N.262, S.263 Ligands: CA.16 13 PLIP interactions: 13 interactions with chain H Hydrogen bonds: H:P.37, H:S.39, H:S.103, H:I.104, H:G.105, H:M.106, H:T.107, H:T.107, H:F.108, H:N.262, H:S.263 pi-Stacking: H:F.108, H:F.108

8 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: T.107, D.130, D.208 Chain B: Y.281 Ligands: ADP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.107 CA.4: 5 residues within 4Å: Chain B: T.107, D.130, D.208 Chain C: Y.281 Ligands: ADP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.107 CA.6: 4 residues within 4Å: Chain C: T.107, D.130 Chain D: Y.281 Ligands: ADP.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.107 CA.8: 4 residues within 4Å: Chain D: T.107, D.130 Chain E: Y.281 Ligands: ADP.7 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.107 CA.10: 5 residues within 4Å: Chain E: M.106, T.107, D.130, D.208 Ligands: ADP.9 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.107 CA.12: 3 residues within 4Å: Chain F: T.107, D.130 Ligands: ADP.11 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.107 CA.14: 4 residues within 4Å: Chain G: T.107, D.130 Chain H: Y.281 Ligands: ADP.13 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:T.107 CA.16: 4 residues within 4Å: Chain H: T.107, D.130, D.208 Ligands: ADP.15 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:T.107

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bechet, E. et al., Identification of structural and molecular determinants of the tyrosine-kinase Wzc and implications in capsular polysaccharide export. Mol.Microbiol. (2010)

Release Date

2010-08-25

Peptides

Tyrosine-protein kinase wzc: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
I

B
J

C
K

D
L

E
M

F
N

G
O

H
P

Tyrosine-protein kinase wzc

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