SMTL ID : 5cnl.3 (2 other biounits)

Crystal structure of an IcmL-like type IV secretion system protein (lpg0120) from Legionella pneumophila subsp. pneumophila str. Philadelphia 1 at 2.65 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

homo-tetramer

Ligands

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

PGE.1: 7 residues within 4Å: Chain A: Y.20, Y.46, A.49, L.50, L.128, Q.129, S.130 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.103, A:S.130 PGE.2: 7 residues within 4Å: Chain A: N.13, I.17, A.68 Chain B: A.70, T.71, E.72, P.73 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.13, A:A.68 Water bridges: B:N.13 PGE.10: 6 residues within 4Å: Chain B: R.5, L.8, L.76, T.78 Ligands: SO4.11, SO4.12 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:P.3, B:T.78, B:T.78 PGE.14: 7 residues within 4Å: Chain C: Y.20, Y.46, A.49, L.50, L.128, Q.129, S.130 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Y.20, C:S.130 PGE.15: 7 residues within 4Å: Chain C: N.13, I.17, A.68 Chain D: A.70, T.71, E.72, P.73 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C Water bridges: D:N.13 Hydrogen bonds: C:N.13, C:A.68 PGE.23: 6 residues within 4Å: Chain D: R.5, L.8, L.76, T.78 Ligands: SO4.24, SO4.25 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:P.3, D:T.78, D:T.78, D:T.78

4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 6 residues within 4Å: Chain A: S.39, A.40, D.41, S.115, Q.118, S.124 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:A.40, A:D.41, A:D.41, A:D.41, A:S.115, A:S.115, A:S.124, A:S.124 PEG.4: 8 residues within 4Å: Chain A: S.53, L.55, V.58, Y.94, Q.101, Q.103 Chain C: Q.101 Ligands: PEG.17 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.53 PEG.16: 6 residues within 4Å: Chain C: S.39, A.40, D.41, S.115, Q.118, S.124 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:A.40, C:D.41, C:D.41, C:S.115, C:S.115, C:S.124, C:S.124 PEG.17: 8 residues within 4Å: Chain A: Q.101 Chain C: S.53, L.55, V.58, Y.94, Q.101, Q.103 Ligands: PEG.4 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.53

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

SO4.5: 4 residues within 4Å: Chain A: L.76, I.77, T.78 Ligands: SO4.9 Ligand excluded by PLIP SO4.6: 3 residues within 4Å: Chain A: G.119, V.120, R.121 Ligand excluded by PLIP SO4.7: 5 residues within 4Å: Chain A: I.133, S.134 Chain C: I.133, S.134 Ligands: SO4.20 Ligand excluded by PLIP SO4.8: 5 residues within 4Å: Chain A: Y.27, Q.31, S.47, L.50, N.51 Ligand excluded by PLIP SO4.9: 3 residues within 4Å: Chain A: R.5, L.76 Ligands: SO4.5 Ligand excluded by PLIP SO4.11: 4 residues within 4Å: Chain B: R.5, K.75, L.76 Ligands: PGE.10 Ligand excluded by PLIP SO4.12: 3 residues within 4Å: Chain B: D.4, R.5 Ligands: PGE.10 Ligand excluded by PLIP SO4.13: 4 residues within 4Å: Chain B: A.49, L.128, Q.129, S.130 Ligand excluded by PLIP SO4.18: 4 residues within 4Å: Chain C: L.76, I.77, T.78 Ligands: SO4.22 Ligand excluded by PLIP SO4.19: 3 residues within 4Å: Chain C: G.119, V.120, R.121 Ligand excluded by PLIP SO4.20: 5 residues within 4Å: Chain A: I.133, S.134 Chain C: I.133, S.134 Ligands: SO4.7 Ligand excluded by PLIP SO4.21: 5 residues within 4Å: Chain C: Y.27, Q.31, S.47, L.50, N.51 Ligand excluded by PLIP SO4.22: 3 residues within 4Å: Chain C: R.5, L.76 Ligands: SO4.18 Ligand excluded by PLIP SO4.24: 4 residues within 4Å: Chain D: R.5, K.75, L.76 Ligands: PGE.23 Ligand excluded by PLIP SO4.25: 3 residues within 4Å: Chain D: D.4, R.5 Ligands: PGE.23 Ligand excluded by PLIP SO4.26: 4 residues within 4Å: Chain D: A.49, L.128, Q.129, S.130 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of an IcmL-like type IV secretion system protein (lpg0120) from Legionella pneumophila subsp. pneumophila str. Philadelphia 1 at 2.65 A resolution. To be published

Release Date

2015-08-05

Peptides

IcmL-like: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

IcmL-like

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