SMTL ID : 6rhw.1

Crystal structure of human CD11b I-domain (CD11b-I) in complex with Staphylococcus aureus octameric bi-component leukocidin LukGH

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

hetero-4-4-4-mer

Ligands

24 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.1: 8 residues within 4Å: Chain A: L.156, L.157, D.158, Q.159, K.169, E.171 Chain K: R.240, S.241 Ligand excluded by PLIP DMS.2: 8 residues within 4Å: Chain A: Y.73, W.74, G.205, N.206, L.207, W.208, W.262, W.271 Ligand excluded by PLIP DMS.3: 9 residues within 4Å: Chain A: N.33, G.62, S.63, G.64, L.65, K.216, E.225 Chain B: G.182, K.183 Ligand excluded by PLIP DMS.4: 11 residues within 4Å: Chain A: K.216, E.225 Chain B: H.112, I.179, S.181, G.182, H.190, S.192, I.194, Y.321, G.324 Ligand excluded by PLIP DMS.5: 8 residues within 4Å: Chain B: D.114, T.265, T.267, R.294, I.296, Y.321 Chain C: F.120 Ligands: DMS.6 Ligand excluded by PLIP DMS.6: 11 residues within 4Å: Chain B: R.294, K.319, P.320, Y.321, K.322, E.323 Chain C: S.18, E.118, F.120 Ligands: DMS.5, MG.7 Ligand excluded by PLIP DMS.8: 8 residues within 4Å: Chain D: L.156, L.157, D.158, Q.159, K.169, E.171 Chain H: R.240, S.241 Ligand excluded by PLIP DMS.9: 8 residues within 4Å: Chain D: Y.73, W.74, G.205, N.206, L.207, W.208, W.262, W.271 Ligand excluded by PLIP DMS.10: 9 residues within 4Å: Chain D: N.33, G.62, S.63, G.64, L.65, K.216, E.225 Chain E: G.182, K.183 Ligand excluded by PLIP DMS.11: 11 residues within 4Å: Chain D: K.216, E.225 Chain E: H.112, I.179, S.181, G.182, H.190, S.192, I.194, Y.321, G.324 Ligand excluded by PLIP DMS.12: 8 residues within 4Å: Chain E: D.114, T.265, T.267, R.294, I.296, Y.321 Chain F: F.120 Ligands: DMS.13 Ligand excluded by PLIP DMS.13: 11 residues within 4Å: Chain E: R.294, K.319, P.320, Y.321, K.322, E.323 Chain F: S.18, E.118, F.120 Ligands: DMS.12, MG.14 Ligand excluded by PLIP DMS.15: 8 residues within 4Å: Chain B: R.240, S.241 Chain G: L.156, L.157, D.158, Q.159, K.169, E.171 Ligand excluded by PLIP DMS.16: 8 residues within 4Å: Chain G: Y.73, W.74, G.205, N.206, L.207, W.208, W.262, W.271 Ligand excluded by PLIP DMS.17: 9 residues within 4Å: Chain G: N.33, G.62, S.63, G.64, L.65, K.216, E.225 Chain H: G.182, K.183 Ligand excluded by PLIP DMS.18: 11 residues within 4Å: Chain G: K.216, E.225 Chain H: H.112, I.179, S.181, G.182, H.190, S.192, I.194, Y.321, G.324 Ligand excluded by PLIP DMS.19: 8 residues within 4Å: Chain H: D.114, T.265, T.267, R.294, I.296, Y.321 Chain I: F.120 Ligands: DMS.20 Ligand excluded by PLIP DMS.20: 11 residues within 4Å: Chain H: R.294, K.319, P.320, Y.321, K.322, E.323 Chain I: S.18, E.118, F.120 Ligands: DMS.19, MG.21 Ligand excluded by PLIP DMS.22: 8 residues within 4Å: Chain E: R.240, S.241 Chain J: L.156, L.157, D.158, Q.159, K.169, E.171 Ligand excluded by PLIP DMS.23: 8 residues within 4Å: Chain J: Y.73, W.74, G.205, N.206, L.207, W.208, W.262, W.271 Ligand excluded by PLIP DMS.24: 9 residues within 4Å: Chain J: N.33, G.62, S.63, G.64, L.65, K.216, E.225 Chain K: G.182, K.183 Ligand excluded by PLIP DMS.25: 11 residues within 4Å: Chain J: K.216, E.225 Chain K: H.112, I.179, S.181, G.182, H.190, S.192, I.194, Y.321, G.324 Ligand excluded by PLIP DMS.26: 8 residues within 4Å: Chain K: D.114, T.265, T.267, R.294, I.296, Y.321 Chain L: F.120 Ligands: DMS.27 Ligand excluded by PLIP DMS.27: 11 residues within 4Å: Chain K: R.294, K.319, P.320, Y.321, K.322, E.323 Chain L: S.18, E.118, F.120 Ligands: DMS.26, MG.28 Ligand excluded by PLIP

4 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 7 residues within 4Å: Chain B: E.323 Chain C: D.14, S.16, S.18, T.83, E.118 Ligands: DMS.6 5 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: C:S.16, C:S.18, C:T.83, B:E.323, H2O.1 MG.14: 7 residues within 4Å: Chain E: E.323 Chain F: D.14, S.16, S.18, T.83, E.118 Ligands: DMS.13 5 PLIP interactions: 1 interactions with chain E, 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: E:E.323, F:S.16, F:S.18, F:T.83, H2O.1 MG.21: 7 residues within 4Å: Chain H: E.323 Chain I: D.14, S.16, S.18, T.83, E.118 Ligands: DMS.20 5 PLIP interactions: 3 interactions with chain I, 1 interactions with chain H, 1 Ligand-Water interactions Metal complexes: I:S.16, I:S.18, I:T.83, H:E.323, H2O.1 MG.28: 7 residues within 4Å: Chain K: E.323 Chain L: D.14, S.16, S.18, T.83, E.118 Ligands: DMS.27 5 PLIP interactions: 3 interactions with chain L, 1 interactions with chain K, 1 Ligand-Water interactions Metal complexes: L:S.16, L:S.18, L:T.83, K:E.323, H2O.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Trstenjak, N. et al., Molecular mechanism of leukocidin GH-integrin CD11b/CD18 recognition and species specificity. Proc.Natl.Acad.Sci.USA (2020)

Release Date

2019-12-18

Peptides

Beta-channel forming cytolysin: ADGJ
Beta-channel forming cytolysin: BEHK
Integrin alpha-M: CFIL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

D
G

G
G

J
G

B
H

E
H

H
H

K
H

C
C

F
C

I
C

L
C

Beta-channel forming cytolysin

Beta-channel forming cytolysin

Integrin alpha-M

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