SMTL ID : 6nhu.3 (2 other biounits)

Crystal Structure of the Beta Lactamase Class D YbxI from Agrobacterium fabrum

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

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

PO4.1: 9 residues within 4Å: Chain A: R.71, T.187, Y.189 Chain B: D.174, A.175, P.176, E.177, S.178 Ligands: EDO.3 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:A.175, B:S.178, A:R.71, A:T.187

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 4 residues within 4Å: Chain A: K.58, T.59, P.60, A.61 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.59, A:A.61 EDO.3: 6 residues within 4Å: Chain A: Y.189, R.191, P.197 Chain B: P.176, E.177 Ligands: PO4.1 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.191, A:R.191, B:E.177, B:S.178 EDO.4: 6 residues within 4Å: Chain B: D.63, W.64, K.65, T.68, W.90, E.94 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.65, B:T.68

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, Y. et al., Crystal Structure of the Beta Lactamase Class D YbxI from Agrobacterium fabrum. To Be Published

Release Date

2019-01-16

Peptides

Beta-lactamase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

Beta-lactamase

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