SMTL ID : 4l6t.1

GM1 bound form of the ECX AB5 holotoxin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

hetero-1-5-mer

Ligands

5 x BGC- GAL- NGA- GAL- SIA: beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-[N-acetyl-alpha-neuraminic acid-(2-3)]beta-D-galactopyranose-(1-4)-beta-D-glucopyranose(Non-covalent)

BGC-GAL-NGA-GAL-SIA.1: 13 residues within 4Å: Chain B: E.12, Y.13, Q.14, N.15, E.52, Q.57, H.58, L.59, Q.62, W.89, N.91, K.92 Chain C: G.34 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain B Water bridges: C:G.34, B:K.92, B:Q.14, B:Q.14, B:N.91, B:Q.62 Hydrogen bonds: B:Q.62, B:Q.62, B:N.91, B:N.91, B:K.92, B:E.12, B:Q.14 Hydrophobic interactions: B:Q.14 BGC-GAL-NGA-GAL-SIA.2: 14 residues within 4Å: Chain C: E.12, Y.13, Q.14, N.15, E.52, Q.57, H.58, L.59, Q.62, W.89, N.91, K.92 Chain D: G.34, K.35 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:E.52, C:Q.62, C:Q.62, C:N.91, C:N.91, C:K.92, C:E.12, C:Q.14 Water bridges: C:L.59, D:G.34, C:Q.14, C:Q.14, C:L.59, C:N.91, C:N.91, C:N.91, C:E.12, C:L.59, C:Q.62 Hydrophobic interactions: C:Q.14 BGC-GAL-NGA-GAL-SIA.3: 13 residues within 4Å: Chain D: E.12, Y.13, Q.14, N.15, E.52, Q.57, H.58, L.59, Q.62, W.89, N.91, K.92 Chain E: G.34 7 PLIP interactions: 6 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:E.52, D:Q.62, D:Q.62, D:N.91, D:N.91, D:K.92, D:E.12, D:Q.14 Water bridges: D:E.52, D:L.59, E:G.34, D:Q.14, D:Q.14, D:L.59, D:N.91, D:N.91, D:N.91, D:E.12, D:Q.14, D:L.59, D:Q.62 Hydrophobic interactions: D:Q.14 BGC-GAL-NGA-GAL-SIA.4: 14 residues within 4Å: Chain E: E.12, Y.13, Q.14, N.15, E.52, Q.57, H.58, L.59, Q.62, W.89, N.91, K.92 Chain F: G.34, K.35 6 PLIP interactions: 5 interactions with chain E, 1 interactions with chain F Water bridges: E:Q.14, E:L.59, E:S.96, F:G.34, E:Q.14, E:Q.14, E:L.59, E:N.91, E:N.91, E:N.91, E:L.59, E:Q.62, E:Q.62 Hydrogen bonds: E:E.52, E:Q.62, E:Q.62, E:N.91, E:N.91, E:K.92, E:E.12, E:Q.14 Hydrophobic interactions: E:Q.14 BGC-GAL-NGA-GAL-SIA.5: 13 residues within 4Å: Chain B: G.34 Chain F: E.12, Y.13, Q.14, N.15, E.52, Q.57, H.58, L.59, Q.62, W.89, N.91, K.92 6 PLIP interactions: 5 interactions with chain F, 1 interactions with chain B Hydrogen bonds: F:Q.62, F:Q.62, F:N.91, F:N.91, F:K.92, F:E.12, F:Q.14 Water bridges: F:L.59, B:G.34, F:Q.14, F:Q.14, F:N.91, F:L.59, F:Q.62 Hydrophobic interactions: F:Q.14, F:E.12

1 x ZN: ZINC ION(Non-covalent)

ZN.6: 3 residues within 4Å: Chain A: H.160, H.164, H.170 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.160, A:H.164, A:H.170, H2O.2

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ng, N.M. et al., EcxAB Is a Founding Member of a New Family of Metalloprotease AB5 Toxins with a Hybrid Cholera-like B Subunit. Structure (2013)

Release Date

2013-11-06

Peptides

ECXA: A
ECXB: BCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

ECXA

ECXB

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