SMTL ID : 5imt.1 (1 other biounit)

Toxin receptor complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-2-2-mer

Ligands

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.1: 11 residues within 4Å: Chain A: W.439, E.441, S.456, W.457, S.458, L.472, R.473, F.474, K.475, N.477, V.478 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.458, A:K.475 PGE.11: 11 residues within 4Å: Chain B: W.439, E.441, S.456, W.457, S.458, L.472, R.473, F.474, K.475, N.477, V.478 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.458, B:K.475

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

SO4.2: 6 residues within 4Å: Chain A: A.206, M.208, Q.257, I.374, Q.375, S.378 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.257 SO4.3: 5 residues within 4Å: Chain A: F.240, S.241, H.244 Chain B: H.91, I.411 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.244 SO4.12: 6 residues within 4Å: Chain B: A.206, M.208, Q.257, I.374, Q.375, S.378 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.257 SO4.13: 5 residues within 4Å: Chain A: H.91, I.411 Chain B: F.240, S.241, H.244 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:H.244 SO4.21: 4 residues within 4Å: Chain C: K.66, C.69, F.71, Q.74 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Q.74 Water bridges: C:K.66, C:K.66 Salt bridges: C:K.66 SO4.24: 4 residues within 4Å: Chain D: K.66, C.69, F.71, Q.74 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Q.74 Water bridges: D:K.66, D:K.66 Salt bridges: D:K.66

14 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain A: E.447 Chain B: H.98, R.99, K.475 5 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:H.98, A:E.447, A:E.447, H2O.1, H2O.5 ZN.5: 4 residues within 4Å: Chain A: H.98, G.101, D.420, R.473 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.420, H2O.3, H2O.4, H2O.4 ZN.6: 4 residues within 4Å: Chain A: H.83, Q.140, E.144, A.227 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.83, A:E.144, H2O.2, H2O.4 ZN.7: 4 residues within 4Å: Chain A: R.94, A.96, H.444, E.450 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.444, A:E.450, A:E.450, H2O.3, H2O.4 ZN.8: 1 residues within 4Å: Chain A: H.467 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.467 ZN.14: 4 residues within 4Å: Chain A: H.98, R.99, K.475 Chain B: E.447 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:E.447, B:E.447, A:H.98, H2O.1, H2O.4 ZN.15: 4 residues within 4Å: Chain B: H.98, G.101, D.420, R.473 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.420, H2O.7, H2O.8, H2O.8 ZN.16: 4 residues within 4Å: Chain B: H.83, Q.140, E.144, A.227 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.83, B:E.144, H2O.6, H2O.8 ZN.17: 4 residues within 4Å: Chain B: R.94, A.96, H.444, E.450 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.444, B:E.450, B:E.450, H2O.7, H2O.8 ZN.18: 1 residues within 4Å: Chain B: H.467 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.467 ZN.22: 4 residues within 4Å: Chain A: G.165, H.202 Chain C: E.73, N.77 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: A:H.202, C:E.73, H2O.4, H2O.9 ZN.23: 3 residues within 4Å: Chain C: K.41, H.44, R.53 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.44, H2O.9 ZN.25: 4 residues within 4Å: Chain B: G.165, H.202 Chain D: E.73, N.77 4 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: D:E.73, B:H.202, H2O.8, H2O.9 ZN.26: 3 residues within 4Å: Chain D: K.41, H.44, R.53 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.44, H2O.9

4 x CU: COPPER (II) ION(Non-covalent)

CU.9: 7 residues within 4Å: Chain A: K.119, N.299, V.300, S.301, S.390, Y.391, T.392 No protein-ligand interaction detected (PLIP) CU.10: 5 residues within 4Å: Chain A: R.99, E.102, K.315, S.417, K.419 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.102, A:E.102, H2O.1, H2O.2, H2O.2 CU.19: 7 residues within 4Å: Chain B: K.119, N.299, V.300, S.301, S.390, Y.391, T.392 No protein-ligand interaction detected (PLIP) CU.20: 5 residues within 4Å: Chain B: R.99, E.102, K.315, S.417, K.419 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.102, B:E.102, H2O.5, H2O.6, H2O.6

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lawrence, S.L. et al., Structural Basis for Receptor Recognition by the Human CD59-Responsive Cholesterol-Dependent Cytolysins. Structure (2016)

Release Date

2016-08-24

Peptides

Intermedilysin: AB
CD59 glycoprotein: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
D

D
D

Intermedilysin

CD59 glycoprotein

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