SMTL ID : 3bvj.1

Crystal Structure of Human Orotidine 5'-monophosphate Decarboxylase Complexed with XMP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: S.180, K.184, H.225 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.180 Water bridges: A:S.180, A:E.224, A:E.224 Salt bridges: A:K.184, A:H.225 SO4.2: 3 residues within 4Å: Chain B: S.180, K.184, H.225 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.180 Salt bridges: B:K.184, B:H.225

2 x XMP: XANTHOSINE-5'-MONOPHOSPHATE(Non-covalent)

XMP.3: 19 residues within 4Å: Chain A: S.89, D.91, K.113, H.115, D.144, K.146, N.173, I.200, M.203, S.204, I.233, P.249, Q.262, Y.264, G.282, R.283 Chain B: D.149, I.150, T.153 20 PLIP interactions: 18 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.89, A:D.91, A:K.113, A:D.144, A:K.146, A:N.173, A:S.204, A:S.204, A:Q.262, A:Y.264, A:Y.264, A:G.282, A:R.283, B:D.149, B:T.153 Water bridges: A:E.202, A:G.250, A:G.250, A:G.284 Salt bridges: A:R.283 XMP.4: 19 residues within 4Å: Chain A: D.149, I.150, T.153 Chain B: S.89, D.91, K.113, H.115, D.144, K.146, N.173, I.200, M.203, S.204, I.233, P.249, Q.262, Y.264, G.282, R.283 18 PLIP interactions: 17 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.89, B:D.91, B:K.113, B:D.144, B:K.146, B:N.173, B:S.204, B:S.204, B:Q.262, B:Y.264, B:G.282, B:R.283, A:D.149 Water bridges: B:E.202, B:G.250, B:V.251, B:G.284 Salt bridges: B:R.283

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 6 residues within 4Å: Chain A: R.67, I.68, H.69, P.70, S.226, E.227 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.68

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, Y. et al., Crystal Structure of Human Orotidine 5'-monophosphate Decarboxylase Complexed with XMP. To be Published

Release Date

2008-11-18

Peptides

Uridine 5'-monophosphate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Uridine 5'-monophosphate synthase

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