SMTL ID : 3uwq.1

1.80 Angstrom resolution crystal structure of orotidine 5'-phosphate decarboxylase from Vibrio cholerae O1 biovar eltor str. N16961 in complex with uridine-5'-monophosphate (UMP)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x U5P: URIDINE-5'-MONOPHOSPHATE(Non-covalent)

U5P.1: 15 residues within 4Å: Chain A: A.33, D.35, K.57, T.144, P.202, G.203, R.205, V.232, I.233, G.234, R.235, P.236 Chain B: I.90, T.93 Ligands: PGE.5 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:P.202 Hydrogen bonds: A:D.35, A:K.57, A:T.144, A:G.234, A:R.235 Water bridges: A:K.86, A:K.86, A:K.86, A:T.144, A:T.144, A:G.203, A:G.203, A:R.205, A:R.235 Salt bridges: A:R.205, A:R.235 U5P.7: 15 residues within 4Å: Chain A: I.90, T.93 Chain B: A.33, D.35, K.57, T.144, P.202, G.203, R.205, V.232, I.233, G.234, R.235, P.236 Ligands: XPE.2 16 PLIP interactions: 15 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.35, B:K.57, B:T.144, B:T.144, B:G.234, B:R.235, A:T.93 Water bridges: B:D.84, B:K.86, B:K.86, B:G.203, B:R.205, B:R.205, B:R.235 Salt bridges: B:R.205, B:R.235

1 x XPE: 3,6,9,12,15,18,21,24,27-NONAOXANONACOSANE-1,29-DIOL(Non-covalent)

XPE.2: 10 residues within 4Å: Chain A: I.90, N.92, S.95, K.96 Chain B: D.35, Y.36, R.235, T.238, Q.239 Ligands: U5P.7 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:N.92, A:S.95, A:K.96, B:R.235, B:R.235 Water bridges: A:N.92, B:T.238

4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 4 residues within 4Å: Chain A: D.35, Y.36, T.238, Q.239 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.238 PEG.4: 3 residues within 4Å: Chain A: H.75, F.79, G.105 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.78 Water bridges: A:H.75, A:L.104 PEG.8: 4 residues within 4Å: Chain B: H.75, G.78, F.79, G.105 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.78 PEG.9: 3 residues within 4Å: Chain B: S.187, K.190, S.226 No protein-ligand interaction detected (PLIP)

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.5: 6 residues within 4Å: Chain A: T.144, S.145, R.235 Chain B: I.90, N.92 Ligands: U5P.1 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:N.92 Hydrogen bonds: A:R.235 PGE.10: 5 residues within 4Å: Chain B: A.102, E.103, G.105, P.129, Y.130 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:P.129

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.6: 4 residues within 4Å: Chain A: L.136, D.177, E.196, K.198 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.177 Water bridges: A:R.134, A:L.176, A:D.177, A:D.177

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Halavaty, A.S. et al., 1.80 Angstrom resolution crystal structure of orotidine 5'-phosphate decarboxylase from Vibrio cholerae O1 biovar eltor str. N16961 in complex with uridine-5'-monophosphate (UMP). To be Published

Release Date

2011-12-14

Peptides

Orotidine 5'-phosphate decarboxylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Orotidine 5'-phosphate decarboxylase

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