SMTL ID : 7vdy.1

Crystal structure of O-ureidoserine racemase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.12 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 7 residues within 4Å: Chain A: N.20, C.81, G.82, N.83, C.227, G.228, S.229 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.20, A:G.82, A:N.83, A:G.228, A:S.229, A:S.229 Water bridges: A:N.167, A:S.229 SO4.2: 4 residues within 4Å: Chain A: P.129, R.130, F.131, A.132 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.130, A:F.131, A:A.132, A:S.135 SO4.3: 4 residues within 4Å: Chain A: A.180, V.182, A.183, R.215 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:V.182, A:A.183 Water bridges: A:R.184, A:R.215, A:R.215, A:R.215, A:E.223 Salt bridges: A:R.215 SO4.4: 6 residues within 4Å: Chain A: R.5, L.10, L.27, P.31, P.33, L.37 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.5 Salt bridges: A:R.5 SO4.5: 4 residues within 4Å: Chain A: R.28, D.29, R.57, E.58 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.29, A:E.58 Salt bridges: A:R.57 SO4.6: 5 residues within 4Å: Chain A: D.176, T.177, A.178, R.205, H.213 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.176, A:T.177, A:T.177, A:A.178 Salt bridges: A:R.205, A:H.213 SO4.7: 3 residues within 4Å: Chain A: H.16, G.254 Chain B: K.46 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Salt bridges: A:H.16, B:K.46 Water bridges: B:K.46, B:K.46 SO4.8: 8 residues within 4Å: Chain B: N.20, C.81, G.82, N.83, E.218, C.227, G.228, S.229 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.82, B:N.83, B:G.228, B:S.229 Water bridges: B:G.84 SO4.9: 3 residues within 4Å: Chain B: V.182, A.183, R.215 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:V.182, B:A.183 Water bridges: B:R.184, B:R.215 Salt bridges: B:R.215 SO4.10: 3 residues within 4Å: Chain B: R.130, F.131, A.132 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:F.131, B:A.132 Water bridges: B:P.129, B:R.130 Salt bridges: B:R.130

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Oda, K. et al., Crystal structure of O-ureidoserine racemase found in the d-cycloserine biosynthetic pathway. Proteins (2022)

Release Date

2021-12-15

Peptides

O-ureido-serine racemase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

O-ureido-serine racemase