SMTL ID : 3ba3.1

Crystal structure of Pyridoxamine 5'-phosphate oxidase-like protein (NP_783940.1) from Lactobacillus plantarum at 1.55 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 6 residues within 4Å: Chain A: G.134, V.135, G.136, G.137, K.139 Ligands: EDO.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.134, A:G.136, A:G.137 Salt bridges: A:K.139 SO4.2: 3 residues within 4Å: Chain A: N.15, K.16, P.106 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.15, B:N.77 Water bridges: A:K.16, A:K.16, A:K.16, A:K.16, A:K.16 Salt bridges: A:K.16

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

EDO.3: 7 residues within 4Å: Chain A: W.112, D.113, A.114, I.115, G.116, S.117, T.118 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:W.112, A:S.117, A:T.118 Water bridges: A:S.117, A:S.117 EDO.4: 3 residues within 4Å: Chain A: K.16, I.31, N.33 3 PLIP interactions: 3 interactions with chain A Water bridges: A:N.15, A:K.16, A:I.31 EDO.5: 4 residues within 4Å: Chain A: G.136, G.137, K.139 Ligands: SO4.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.136 EDO.6: 3 residues within 4Å: Chain A: Y.37, K.92, D.96 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.96 EDO.7: 5 residues within 4Å: Chain A: L.102, E.103, T.104, V.105, P.106 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.104 Water bridges: A:N.15, A:N.107 EDO.8: 2 residues within 4Å: Chain A: R.81 Chain B: K.30 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.81, B:K.30 EDO.9: 7 residues within 4Å: Chain B: W.112, D.113, A.114, I.115, G.116, S.117, T.118 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:W.112, B:S.117 Water bridges: B:A.114, B:G.116, B:S.117 EDO.10: 4 residues within 4Å: Chain B: Y.37, K.92, D.96 Ligands: EDO.12 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.96 Water bridges: B:K.92, B:K.92 EDO.11: 3 residues within 4Å: Chain B: K.16, I.31, N.33 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.33 EDO.12: 6 residues within 4Å: Chain B: Y.37, A.39, Q.40, Y.45, K.92 Ligands: EDO.10 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.45, B:Y.45 Water bridges: B:K.92

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of Pyridoxamine 5'-phosphate oxidase-like protein (NP_783940.1) from Lactobacillus plantarum at 1.55 A resolution. To be published

Release Date

2007-11-20

Peptides

Pyridoxamine 5'-phosphate oxidase-like protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Pyridoxamine 5'-phosphate oxidase-like protein