SMTL ID : 8h09.2 (1 other biounit)

Structure of the thermolabile hemolysin from Vibrio alginolyticus (apo form)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.81 Å

Oligo State

monomer

Ligands

3 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.1: 15 residues within 4Å: Chain A: D.154, S.155, L.156, F.170, G.206, L.249, N.250, M.253, N.254, P.287, A.289, A.292, F.390, T.394, H.395 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.155, A:N.250 Water bridges: A:G.206, A:T.394 1PE.2: 9 residues within 4Å: Chain A: F.89, K.90, Y.130, N.161, N.164, A.165, Q.167, T.217 Ligands: 1PS.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.90 1PE.3: 3 residues within 4Å: Chain A: A.319, M.322, Y.323 No protein-ligand interaction detected (PLIP)

2 x 1PS: 3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE(Non-covalent)

1PS.4: 10 residues within 4Å: Chain A: K.90, N.91, M.92, T.133, N.161, N.201, W.202, S.225, Y.229 Ligands: 1PE.2 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.202 Hydrogen bonds: A:S.225, A:Y.229 pi-Stacking: A:W.202, A:Y.229 1PS.5: 6 residues within 4Å: Chain A: R.127, Y.128, S.129, Y.130, Q.167, W.168 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.130, A:Y.130 Salt bridges: A:R.127 pi-Stacking: A:W.168, A:W.168

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

PEG.6: 6 residues within 4Å: Chain A: R.103, E.189, A.192, K.193, N.196, L.197 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.103, A:R.103, A:K.193, A:K.193 Water bridges: A:L.199

1 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 2 residues within 4Å: Chain A: E.210, D.265 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.210, A:D.265, H2O.2, H2O.2, H2O.3

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, C. et al., Catalytic site flexibility facilitates the substrate and catalytic promiscuity of Vibrio dual lipase/transferase. Nat Commun (2023)

Release Date

2023-08-16

Peptides

SGNH/GDSL hydrolase family protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

SGNH/GDSL hydrolase family protein

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