SMTL ID : 3naw.3 (2 other biounits)

Crystal structure of E. coli O157:H7 effector protein NleL

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 6 residues within 4Å: Chain A: R.315, D.316, G.317, M.318, Q.319, E.320 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.317, A:Q.319, A:Q.319, A:E.320 Water bridges: A:G.317 SO4.2: 7 residues within 4Å: Chain A: K.597, F.604, R.613 Chain B: Y.290, G.296, A.297, S.300 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:R.613, B:Y.290, B:S.300, B:S.300 Salt bridges: A:K.597, A:R.613 SO4.3: 4 residues within 4Å: Chain A: E.451, R.455, Y.467, K.477 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.451, A:E.451, A:Y.467 Water bridges: A:K.477 Salt bridges: A:R.455, A:K.477 SO4.4: 1 residues within 4Å: Chain A: R.455 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.455 SO4.9: 4 residues within 4Å: Chain B: G.317, M.318, Q.319, E.320 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.317, B:M.318, B:Q.319, B:E.320 Water bridges: B:E.320 SO4.10: 5 residues within 4Å: Chain B: S.414, L.415, S.416, Y.430, H.503 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:L.415, B:S.416, B:Y.430 Water bridges: B:N.417 Salt bridges: B:H.503 SO4.11: 2 residues within 4Å: Chain B: A.479, N.483 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.483 SO4.12: 4 residues within 4Å: Chain B: T.392, S.393, T.394, N.395 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.395

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 4 residues within 4Å: Chain A: E.320, R.323, E.324, E.327 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.323, A:E.324, A:E.327 GOL.6: 7 residues within 4Å: Chain A: Y.232, M.235, W.270 Chain B: F.271, I.275, M.277 Ligands: GOL.15 No protein-ligand interaction detected (PLIP) GOL.7: 2 residues within 4Å: Chain A: R.578, N.579 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.579 GOL.8: 4 residues within 4Å: Chain A: R.65, N.85, E.86 Chain B: D.204 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.204, A:N.85 Water bridges: B:D.204 GOL.13: 5 residues within 4Å: Chain A: Y.188 Chain B: N.187, Y.188, E.280 Ligands: GOL.14 No protein-ligand interaction detected (PLIP) GOL.14: 5 residues within 4Å: Chain A: N.187, Y.188, E.280 Chain B: Y.188 Ligands: GOL.13 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.187, A:Y.188 GOL.15: 6 residues within 4Å: Chain A: F.271, M.277 Chain B: P.231, Y.232, W.270 Ligands: GOL.6 No protein-ligand interaction detected (PLIP) GOL.16: 4 residues within 4Å: Chain B: R.230, P.231, Y.232, V.233 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.230, B:R.230, B:Y.232, B:V.233 GOL.17: 4 residues within 4Å: Chain B: W.396, M.397, Y.430, F.434 No protein-ligand interaction detected (PLIP)

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.18: 5 residues within 4Å: Chain A: D.203, D.204 Chain B: R.65, N.85, E.86 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.85, A:D.204, A:D.204 Salt bridges: B:E.86

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lin, D.Y. et al., Biochemical and Structural Studies of a HECT-like Ubiquitin Ligase from Escherichia coli O157:H7. J.Biol.Chem. (2011)

Release Date

2010-10-27

Peptides

secreted effector protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

secreted effector protein

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