SMTL ID : 4azv.1

Co-crystal structure of WbdD and kinase inhibitor GW435821x.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.29 Å

Oligo State

homo-12-mer

Ligands

12 x SAM: S-ADENOSYLMETHIONINE(Non-covalent)

SAM.1: 22 residues within 4Å: Chain A: Y.29, Q.30, R.49, G.74, C.75, A.76, F.80, I.94, D.95, F.96, Q.97, N.100, G.121, R.122, I.123, E.124, L.141, S.142, V.143, H.145, H.146, I.147 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:Y.29, A:A.76 Hydrogen bonds: A:Q.30, A:G.74, A:A.76, A:D.95, A:D.95, A:F.96, A:Q.97, A:Q.97, A:N.100, A:I.123, A:E.124 Salt bridges: A:R.49 pi-Stacking: A:F.96, A:F.96 pi-Cation interactions: A:Y.29 SAM.7: 22 residues within 4Å: Chain B: Y.29, Q.30, R.49, G.74, C.75, A.76, F.80, I.94, D.95, F.96, Q.97, N.100, G.121, R.122, I.123, E.124, L.141, S.142, V.143, H.145, H.146, I.147 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:Y.29, B:A.76 Hydrogen bonds: B:Q.30, B:G.74, B:A.76, B:D.95, B:D.95, B:F.96, B:Q.97, B:Q.97, B:N.100, B:I.123, B:E.124 Salt bridges: B:R.49 pi-Stacking: B:F.96, B:F.96 pi-Cation interactions: B:Y.29 SAM.13: 22 residues within 4Å: Chain C: Y.29, Q.30, R.49, G.74, C.75, A.76, F.80, I.94, D.95, F.96, Q.97, N.100, G.121, R.122, I.123, E.124, L.141, S.142, V.143, H.145, H.146, I.147 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:Y.29, C:A.76 Hydrogen bonds: C:Q.30, C:G.74, C:A.76, C:D.95, C:D.95, C:F.96, C:Q.97, C:Q.97, C:N.100, C:I.123, C:E.124 Salt bridges: C:R.49 pi-Stacking: C:F.96, C:F.96 pi-Cation interactions: C:Y.29 SAM.19: 22 residues within 4Å: Chain D: Y.29, Q.30, R.49, G.74, C.75, A.76, F.80, I.94, D.95, F.96, Q.97, N.100, G.121, R.122, I.123, E.124, L.141, S.142, V.143, H.145, H.146, I.147 17 PLIP interactions: 17 interactions with chain D Hydrophobic interactions: D:Y.29, D:A.76 Hydrogen bonds: D:Q.30, D:G.74, D:A.76, D:D.95, D:D.95, D:F.96, D:Q.97, D:Q.97, D:N.100, D:I.123, D:E.124 Salt bridges: D:R.49 pi-Stacking: D:F.96, D:F.96 pi-Cation interactions: D:Y.29 SAM.25: 22 residues within 4Å: Chain E: Y.29, Q.30, R.49, G.74, C.75, A.76, F.80, I.94, D.95, F.96, Q.97, N.100, G.121, R.122, I.123, E.124, L.141, S.142, V.143, H.145, H.146, I.147 17 PLIP interactions: 17 interactions with chain E Hydrophobic interactions: E:Y.29, E:A.76 Hydrogen bonds: E:Q.30, E:G.74, E:A.76, E:D.95, E:D.95, E:F.96, E:Q.97, E:Q.97, E:N.100, E:I.123, E:E.124 Salt bridges: E:R.49 pi-Stacking: E:F.96, E:F.96 pi-Cation interactions: E:Y.29 SAM.31: 22 residues within 4Å: Chain F: Y.29, Q.30, R.49, G.74, C.75, A.76, F.80, I.94, D.95, F.96, Q.97, N.100, G.121, R.122, I.123, E.124, L.141, S.142, V.143, H.145, H.146, I.147 17 PLIP interactions: 17 interactions with chain F Hydrophobic interactions: F:Y.29, F:A.76 Hydrogen bonds: F:Q.30, F:G.74, F:A.76, F:D.95, F:D.95, F:F.96, F:Q.97, F:Q.97, F:N.100, F:I.123, F:E.124 Salt bridges: F:R.49 pi-Stacking: F:F.96, F:F.96 pi-Cation interactions: F:Y.29 SAM.37: 22 residues within 4Å: Chain G: Y.29, Q.30, R.49, G.74, C.75, A.76, F.80, I.94, D.95, F.96, Q.97, N.100, G.121, R.122, I.123, E.124, L.141, S.142, V.143, H.145, H.146, I.147 17 PLIP interactions: 17 interactions with chain G Hydrophobic interactions: G:Y.29, G:A.76 Hydrogen bonds: G:Q.30, G:G.74, G:A.76, G:D.95, G:D.95, G:F.96, G:Q.97, G:Q.97, G:N.100, G:I.123, G:E.124 Salt bridges: G:R.49 pi-Stacking: G:F.96, G:F.96 pi-Cation interactions: G:Y.29 SAM.43: 22 residues within 4Å: Chain H: Y.29, Q.30, R.49, G.74, C.75, A.76, F.80, I.94, D.95, F.96, Q.97, N.100, G.121, R.122, I.123, E.124, L.141, S.142, V.143, H.145, H.146, I.147 17 PLIP interactions: 17 interactions with chain H Hydrophobic interactions: H:Y.29, H:A.76 Hydrogen bonds: H:Q.30, H:G.74, H:A.76, H:D.95, H:D.95, H:F.96, H:Q.97, H:Q.97, H:N.100, H:I.123, H:E.124 Salt bridges: H:R.49 pi-Stacking: H:F.96, H:F.96 pi-Cation interactions: H:Y.29 SAM.49: 22 residues within 4Å: Chain I: Y.29, Q.30, R.49, G.74, C.75, A.76, F.80, I.94, D.95, F.96, Q.97, N.100, G.121, R.122, I.123, E.124, L.141, S.142, V.143, H.145, H.146, I.147 17 PLIP interactions: 17 interactions with chain I Hydrophobic interactions: I:Y.29, I:A.76 Hydrogen bonds: I:Q.30, I:G.74, I:A.76, I:D.95, I:D.95, I:F.96, I:Q.97, I:Q.97, I:N.100, I:I.123, I:E.124 Salt bridges: I:R.49 pi-Stacking: I:F.96, I:F.96 pi-Cation interactions: I:Y.29 SAM.55: 22 residues within 4Å: Chain J: Y.29, Q.30, R.49, G.74, C.75, A.76, F.80, I.94, D.95, F.96, Q.97, N.100, G.121, R.122, I.123, E.124, L.141, S.142, V.143, H.145, H.146, I.147 17 PLIP interactions: 17 interactions with chain J Hydrophobic interactions: J:Y.29, J:A.76 Hydrogen bonds: J:Q.30, J:G.74, J:A.76, J:D.95, J:D.95, J:F.96, J:Q.97, J:Q.97, J:N.100, J:I.123, J:E.124 Salt bridges: J:R.49 pi-Stacking: J:F.96, J:F.96 pi-Cation interactions: J:Y.29 SAM.61: 22 residues within 4Å: Chain K: Y.29, Q.30, R.49, G.74, C.75, A.76, F.80, I.94, D.95, F.96, Q.97, N.100, G.121, R.122, I.123, E.124, L.141, S.142, V.143, H.145, H.146, I.147 17 PLIP interactions: 17 interactions with chain K Hydrophobic interactions: K:Y.29, K:A.76 Hydrogen bonds: K:Q.30, K:G.74, K:A.76, K:D.95, K:D.95, K:F.96, K:Q.97, K:Q.97, K:N.100, K:I.123, K:E.124 Salt bridges: K:R.49 pi-Stacking: K:F.96, K:F.96 pi-Cation interactions: K:Y.29 SAM.67: 22 residues within 4Å: Chain L: Y.29, Q.30, R.49, G.74, C.75, A.76, F.80, I.94, D.95, F.96, Q.97, N.100, G.121, R.122, I.123, E.124, L.141, S.142, V.143, H.145, H.146, I.147 17 PLIP interactions: 17 interactions with chain L Hydrophobic interactions: L:Y.29, L:A.76 Hydrogen bonds: L:Q.30, L:G.74, L:A.76, L:D.95, L:D.95, L:F.96, L:Q.97, L:Q.97, L:N.100, L:I.123, L:E.124 Salt bridges: L:R.49 pi-Stacking: L:F.96, L:F.96 pi-Cation interactions: L:Y.29

48 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 8 residues within 4Å: Chain A: R.44, D.45, C.46, N.47, Q.48, R.49, F.207, D.208 Ligand excluded by PLIP SO4.3: 2 residues within 4Å: Chain A: S.347, R.350 Ligand excluded by PLIP SO4.4: 11 residues within 4Å: Chain A: P.180, F.181, Y.182, W.183 Chain B: F.181, Y.182 Chain J: P.180, F.181, Y.182 Ligands: SO4.10, SO4.58 Ligand excluded by PLIP SO4.5: 5 residues within 4Å: Chain A: I.339, D.340, R.341, E.342, W.435 Ligand excluded by PLIP SO4.8: 8 residues within 4Å: Chain B: R.44, D.45, C.46, N.47, Q.48, R.49, F.207, D.208 Ligand excluded by PLIP SO4.9: 2 residues within 4Å: Chain B: S.347, R.350 Ligand excluded by PLIP SO4.10: 11 residues within 4Å: Chain A: P.180, F.181, Y.182 Chain B: P.180, F.181, Y.182, W.183 Chain J: F.181, Y.182 Ligands: SO4.4, SO4.58 Ligand excluded by PLIP SO4.11: 5 residues within 4Å: Chain B: I.339, D.340, R.341, E.342, W.435 Ligand excluded by PLIP SO4.14: 8 residues within 4Å: Chain C: R.44, D.45, C.46, N.47, Q.48, R.49, F.207, D.208 Ligand excluded by PLIP SO4.15: 2 residues within 4Å: Chain C: S.347, R.350 Ligand excluded by PLIP SO4.16: 11 residues within 4Å: Chain C: P.180, F.181, Y.182, W.183 Chain F: F.181, Y.182 Chain I: P.180, F.181, Y.182 Ligands: SO4.34, SO4.52 Ligand excluded by PLIP SO4.17: 5 residues within 4Å: Chain C: I.339, D.340, R.341, E.342, W.435 Ligand excluded by PLIP SO4.20: 8 residues within 4Å: Chain D: R.44, D.45, C.46, N.47, Q.48, R.49, F.207, D.208 Ligand excluded by PLIP SO4.21: 2 residues within 4Å: Chain D: S.347, R.350 Ligand excluded by PLIP SO4.22: 11 residues within 4Å: Chain D: P.180, F.181, Y.182, W.183 Chain E: P.180, F.181, Y.182 Chain K: F.181, Y.182 Ligands: SO4.28, SO4.64 Ligand excluded by PLIP SO4.23: 5 residues within 4Å: Chain D: I.339, D.340, R.341, E.342, W.435 Ligand excluded by PLIP SO4.26: 8 residues within 4Å: Chain E: R.44, D.45, C.46, N.47, Q.48, R.49, F.207, D.208 Ligand excluded by PLIP SO4.27: 2 residues within 4Å: Chain E: S.347, R.350 Ligand excluded by PLIP SO4.28: 11 residues within 4Å: Chain D: F.181, Y.182 Chain E: P.180, F.181, Y.182, W.183 Chain K: P.180, F.181, Y.182 Ligands: SO4.22, SO4.64 Ligand excluded by PLIP SO4.29: 5 residues within 4Å: Chain E: I.339, D.340, R.341, E.342, W.435 Ligand excluded by PLIP SO4.32: 8 residues within 4Å: Chain F: R.44, D.45, C.46, N.47, Q.48, R.49, F.207, D.208 Ligand excluded by PLIP SO4.33: 2 residues within 4Å: Chain F: S.347, R.350 Ligand excluded by PLIP SO4.34: 11 residues within 4Å: Chain C: P.180, F.181, Y.182 Chain F: P.180, F.181, Y.182, W.183 Chain I: F.181, Y.182 Ligands: SO4.16, SO4.52 Ligand excluded by PLIP SO4.35: 5 residues within 4Å: Chain F: I.339, D.340, R.341, E.342, W.435 Ligand excluded by PLIP SO4.38: 8 residues within 4Å: Chain G: R.44, D.45, C.46, N.47, Q.48, R.49, F.207, D.208 Ligand excluded by PLIP SO4.39: 2 residues within 4Å: Chain G: S.347, R.350 Ligand excluded by PLIP SO4.40: 11 residues within 4Å: Chain G: P.180, F.181, Y.182, W.183 Chain H: P.180, F.181, Y.182 Chain L: F.181, Y.182 Ligands: SO4.46, SO4.70 Ligand excluded by PLIP SO4.41: 5 residues within 4Å: Chain G: I.339, D.340, R.341, E.342, W.435 Ligand excluded by PLIP SO4.44: 8 residues within 4Å: Chain H: R.44, D.45, C.46, N.47, Q.48, R.49, F.207, D.208 Ligand excluded by PLIP SO4.45: 2 residues within 4Å: Chain H: S.347, R.350 Ligand excluded by PLIP SO4.46: 11 residues within 4Å: Chain G: F.181, Y.182 Chain H: P.180, F.181, Y.182, W.183 Chain L: P.180, F.181, Y.182 Ligands: SO4.40, SO4.70 Ligand excluded by PLIP SO4.47: 5 residues within 4Å: Chain H: I.339, D.340, R.341, E.342, W.435 Ligand excluded by PLIP SO4.50: 8 residues within 4Å: Chain I: R.44, D.45, C.46, N.47, Q.48, R.49, F.207, D.208 Ligand excluded by PLIP SO4.51: 2 residues within 4Å: Chain I: S.347, R.350 Ligand excluded by PLIP SO4.52: 11 residues within 4Å: Chain C: F.181, Y.182 Chain F: P.180, F.181, Y.182 Chain I: P.180, F.181, Y.182, W.183 Ligands: SO4.16, SO4.34 Ligand excluded by PLIP SO4.53: 5 residues within 4Å: Chain I: I.339, D.340, R.341, E.342, W.435 Ligand excluded by PLIP SO4.56: 8 residues within 4Å: Chain J: R.44, D.45, C.46, N.47, Q.48, R.49, F.207, D.208 Ligand excluded by PLIP SO4.57: 2 residues within 4Å: Chain J: S.347, R.350 Ligand excluded by PLIP SO4.58: 11 residues within 4Å: Chain A: F.181, Y.182 Chain B: P.180, F.181, Y.182 Chain J: P.180, F.181, Y.182, W.183 Ligands: SO4.4, SO4.10 Ligand excluded by PLIP SO4.59: 5 residues within 4Å: Chain J: I.339, D.340, R.341, E.342, W.435 Ligand excluded by PLIP SO4.62: 8 residues within 4Å: Chain K: R.44, D.45, C.46, N.47, Q.48, R.49, F.207, D.208 Ligand excluded by PLIP SO4.63: 2 residues within 4Å: Chain K: S.347, R.350 Ligand excluded by PLIP SO4.64: 11 residues within 4Å: Chain D: P.180, F.181, Y.182 Chain E: F.181, Y.182 Chain K: P.180, F.181, Y.182, W.183 Ligands: SO4.22, SO4.28 Ligand excluded by PLIP SO4.65: 5 residues within 4Å: Chain K: I.339, D.340, R.341, E.342, W.435 Ligand excluded by PLIP SO4.68: 8 residues within 4Å: Chain L: R.44, D.45, C.46, N.47, Q.48, R.49, F.207, D.208 Ligand excluded by PLIP SO4.69: 2 residues within 4Å: Chain L: S.347, R.350 Ligand excluded by PLIP SO4.70: 11 residues within 4Å: Chain G: P.180, F.181, Y.182 Chain H: F.181, Y.182 Chain L: P.180, F.181, Y.182, W.183 Ligands: SO4.40, SO4.46 Ligand excluded by PLIP SO4.71: 5 residues within 4Å: Chain L: I.339, D.340, R.341, E.342, W.435 Ligand excluded by PLIP

12 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 7 residues within 4Å: Chain A: S.142, V.143, F.144, H.145, E.173, L.174, A.175 Ligand excluded by PLIP CL.12: 7 residues within 4Å: Chain B: S.142, V.143, F.144, H.145, E.173, L.174, A.175 Ligand excluded by PLIP CL.18: 7 residues within 4Å: Chain C: S.142, V.143, F.144, H.145, E.173, L.174, A.175 Ligand excluded by PLIP CL.24: 7 residues within 4Å: Chain D: S.142, V.143, F.144, H.145, E.173, L.174, A.175 Ligand excluded by PLIP CL.30: 7 residues within 4Å: Chain E: S.142, V.143, F.144, H.145, E.173, L.174, A.175 Ligand excluded by PLIP CL.36: 7 residues within 4Å: Chain F: S.142, V.143, F.144, H.145, E.173, L.174, A.175 Ligand excluded by PLIP CL.42: 7 residues within 4Å: Chain G: S.142, V.143, F.144, H.145, E.173, L.174, A.175 Ligand excluded by PLIP CL.48: 7 residues within 4Å: Chain H: S.142, V.143, F.144, H.145, E.173, L.174, A.175 Ligand excluded by PLIP CL.54: 7 residues within 4Å: Chain I: S.142, V.143, F.144, H.145, E.173, L.174, A.175 Ligand excluded by PLIP CL.60: 7 residues within 4Å: Chain J: S.142, V.143, F.144, H.145, E.173, L.174, A.175 Ligand excluded by PLIP CL.66: 7 residues within 4Å: Chain K: S.142, V.143, F.144, H.145, E.173, L.174, A.175 Ligand excluded by PLIP CL.72: 7 residues within 4Å: Chain L: S.142, V.143, F.144, H.145, E.173, L.174, A.175 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hagelueken, G. et al., Structure of Wbdd; a Bifunctional Kinase and Methyltransferase that Regulates the Chain Length of the O Antigen in Escherichia Coli O9A. Mol.Microbiol. (2012)

Release Date

2012-09-26

Peptides

WBDD: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

G
A

H
A

I
A

J
A

K
A

L
A

WBDD

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