SMTL ID : 5h3a.1

Structural analysis of KSHV thymidylate synthase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

2 x D16: TOMUDEX(Non-covalent)

D16.1: 8 residues within 4Å: Chain A: F.54, I.82, D.192, L.195, G.196, F.199, Y.232 Ligands: UMP.2 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.54, A:F.199, A:Y.232 Hydrogen bonds: A:G.196 Water bridges: A:F.54 pi-Stacking: A:F.199 D16.3: 8 residues within 4Å: Chain B: F.54, I.82, D.192, L.195, G.196, F.199, Y.232 Ligands: UMP.4 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.199, B:Y.232 Hydrogen bonds: B:D.192, B:G.196 Salt bridges: B:K.51 pi-Stacking: B:F.199

2 x UMP: 2'-DEOXYURIDINE 5'-MONOPHOSPHATE(Non-covalent)

UMP.2: 14 residues within 4Å: Chain A: C.169, H.170, Q.188, R.189, S.190, G.191, D.192, G.196, N.200, H.230, Y.232 Chain B: R.149, R.150 Ligands: D16.1 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Q.188, A:S.190, A:D.192, A:N.200, A:N.200, A:H.230, A:Y.232 Salt bridges: A:R.189, B:R.149, B:R.150 UMP.4: 14 residues within 4Å: Chain A: R.149, R.150 Chain B: C.169, H.170, Q.188, R.189, S.190, G.191, D.192, G.196, N.200, H.230, Y.232 Ligands: D16.3 11 PLIP interactions: 9 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:D.192 Hydrogen bonds: B:H.170, B:Q.188, B:S.190, B:D.192, B:N.200, B:N.200, B:H.230 Salt bridges: B:R.189, A:R.149, A:R.150

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Choi, Y.M. et al., Structural Analysis of Thymidylate Synthase from Kaposi's Sarcoma-Associated Herpesvirus with the Anticancer Drug Raltitrexed. PLoS ONE (2016)

Release Date

2017-01-18

Peptides

ORF70: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

ORF70