SMTL ID : 2r2d.1 (9 other biounits)

Structure of a quorum-quenching lactonase (AiiB) from Agrobacterium tumefaciens

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: D.115, H.116, D.213, H.259 Ligands: PO4.3, GOL.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.116, A:D.213, A:D.213, A:H.259 ZN.2: 5 residues within 4Å: Chain A: H.111, H.113, H.191, D.213 Ligands: PO4.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.111, A:H.113, A:H.191, A:D.213 ZN.7: 5 residues within 4Å: Chain B: D.115, H.116, D.213, H.259 Ligands: PO4.9 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.116, B:D.213, B:D.213, B:H.259 ZN.8: 5 residues within 4Å: Chain B: H.111, H.113, H.191, D.213 Ligands: PO4.9 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.111, B:H.113, B:H.191, B:D.213

3 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 12 residues within 4Å: Chain A: H.111, H.113, N.114, D.115, H.116, H.191, D.213, Y.216, H.259 Ligands: ZN.1, ZN.2, GOL.4 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.114, A:Y.216 Water bridges: A:N.114, A:Y.216 Salt bridges: A:H.113, A:H.116, A:H.191, A:H.259 PO4.9: 12 residues within 4Å: Chain B: H.111, H.113, N.114, D.115, H.116, H.191, D.213, Y.216, H.259 Ligands: ZN.7, ZN.8, GOL.11 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:N.114, B:D.115 Water bridges: B:Y.216, B:Y.216, B:Y.216, B:Y.216 Salt bridges: B:H.113, B:H.116, B:H.191 PO4.10: 4 residues within 4Å: Chain B: H.243, Q.246, Y.247, R.251 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.246, B:Q.246, B:Q.246 Water bridges: B:R.251 Salt bridges: B:R.251

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 8 residues within 4Å: Chain A: I.13, V.15, I.41, N.114, D.115, H.259 Ligands: ZN.1, PO4.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.114 GOL.5: 4 residues within 4Å: Chain A: F.208, S.266, L.267, Y.275 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.266, A:S.266, A:Y.275 GOL.6: 1 residues within 4Å: Chain A: I.83 No protein-ligand interaction detected (PLIP) GOL.11: 7 residues within 4Å: Chain B: I.13, V.15, I.41, N.114, D.115, H.259 Ligands: PO4.9 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.114

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, D. et al., Structure and specificity of a quorum-quenching lactonase (AiiB) from Agrobacterium tumefaciens. Biochemistry (2007)

Release Date

2007-10-09

Peptides

Zn-dependent hydrolases: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
E

Zn-dependent hydrolases

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