SMTL ID : 4owk.1 (7 other biounits)

Crystal Structure of the Vibrio vulnificus Hemolysin/Cytolysin Beta-Trefoil Lectin with N-Acetyl-D-Galactosamine Bound

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-heptamer

Ligands

7 x NGA: 2-acetamido-2-deoxy-beta-D-galactopyranose(Non-covalent)

NGA.1: 9 residues within 4Å: Chain A: D.20, V.21, Y.22, K.28, W.38, H.41, S.43, N.45, Q.46 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.28, A:H.41, A:N.45, A:Q.46 Salt bridges: A:K.28 NGA.3: 8 residues within 4Å: Chain B: D.20, V.21, Y.22, K.28, W.38, H.41, N.45, Q.46 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.28, B:H.41, B:N.45, B:N.45 Salt bridges: B:K.28 NGA.4: 9 residues within 4Å: Chain C: D.20, V.21, Y.22, K.28, W.38, H.41, S.43, N.45, Q.46 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:K.28, C:H.41, C:N.45 Salt bridges: C:K.28 NGA.6: 9 residues within 4Å: Chain D: D.20, V.21, Y.22, K.28, W.38, H.41, S.43, N.45, Q.46 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:K.28, D:H.41, D:N.45, D:Q.46 Salt bridges: D:K.28 NGA.8: 9 residues within 4Å: Chain E: D.20, V.21, Y.22, K.28, W.38, H.41, S.43, N.45, Q.46 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:K.28, E:H.41, E:N.45, E:N.45 Water bridges: E:W.38 Salt bridges: E:K.28 NGA.10: 9 residues within 4Å: Chain F: D.20, V.21, Y.22, K.28, W.38, H.41, S.43, N.45, Q.46 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:K.28, F:H.41, F:N.45 Salt bridges: F:K.28 NGA.12: 9 residues within 4Å: Chain G: D.20, V.21, Y.22, K.28, W.38, H.41, S.43, N.45, Q.46 9 PLIP interactions: 9 interactions with chain G Hydrogen bonds: G:V.21, G:H.41, G:N.45, G:N.45, G:Q.46 Water bridges: G:K.28, G:K.28, G:N.45 Salt bridges: G:K.28

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: W.89, G.91, D.92, K.130, P.131 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.91 GOL.5: 5 residues within 4Å: Chain C: W.89, G.91, D.92, K.130, P.131 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.91 Water bridges: C:G.91 GOL.7: 5 residues within 4Å: Chain D: W.89, G.91, D.92, K.130, P.131 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:G.91 GOL.9: 6 residues within 4Å: Chain E: W.89, G.91, D.92, W.129, K.130, P.131 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:G.91, E:G.91 GOL.11: 5 residues within 4Å: Chain F: W.89, G.91, D.92, K.130, P.131 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:G.91 GOL.13: 5 residues within 4Å: Chain G: W.89, G.91, D.92, K.130, P.131 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:G.91 Water bridges: G:W.89

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Kaus, K. et al., Glycan Specificity of the Vibrio vulnificus Hemolysin Lectin Outlines Evolutionary History of Membrane Targeting by a Toxin Family. J.Mol.Biol. (2014)

Release Date

2014-05-28

Peptides

Cytolysin: ABCDEFG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

Cytolysin

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