SMTL ID : 6nhu.1 (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-tetramer

Ligands

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 7 residues within 4Å: Chain A: S.38, K.41, D.86, K.184, T.185, G.186, T.187 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.38, A:S.38, A:D.86, A:K.184, A:T.187, A:T.187, A:T.187

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

PO4.2: 9 residues within 4Å: Chain B: R.71, T.187, Y.189 Chain D: D.174, A.175, P.176, E.177, S.178 Ligands: EDO.4 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:A.175, D:S.178, B:R.71, B:T.187 PO4.5: 7 residues within 4Å: Chain A: R.71, T.187, Y.189 Chain C: A.175, P.176, E.177, S.178 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:A.175, C:S.178 Water bridges: C:E.177 Salt bridges: A:R.71

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

EDO.3: 4 residues within 4Å: Chain B: K.58, T.59, P.60, A.61 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.59, B:A.61 EDO.4: 6 residues within 4Å: Chain B: Y.189, R.191, P.197 Chain D: P.176, E.177 Ligands: PO4.2 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:E.177, D:S.178, B:R.191, B:R.191 EDO.6: 5 residues within 4Å: Chain C: D.63, W.64, K.65, T.68, W.90 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.65, C:T.68 EDO.7: 6 residues within 4Å: Chain D: D.63, W.64, K.65, T.68, W.90, E.94 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.65, D: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: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Beta-lactamase

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