SMTL ID : 1brw.1

THE CRYSTAL STRUCTURE OF PYRIMIDINE NUCLEOSIDE PHOSPHORYLASE IN A CLOSED CONFORMATION

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 7 residues within 4Å: Chain A: K.81, H.82, S.83, T.92, K.108, S.110, T.120 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:S.83, A:T.120, A:T.120 Water bridges: A:H.82, A:T.92, A:G.111, A:G.111 Salt bridges: A:K.81, A:H.82, A:K.108 PO4.2: 7 residues within 4Å: Chain B: K.81, H.82, S.83, T.92, K.108, S.110, T.120 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:S.83, B:T.92, B:T.92, B:T.92 Water bridges: B:T.92 Salt bridges: B:K.81, B:H.82, B:K.108

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 5 residues within 4Å: Chain A: G.88, T.90, L.243, A.246, E.255 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:G.88, A:T.90, A:L.243, A:A.246, A:E.255 CA.4: 6 residues within 4Å: Chain B: G.88, T.90, L.243, A.246, E.252, E.255 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:G.88, B:T.90, B:L.243, B:A.246, B:E.255

1 x URA: URACIL(Non-covalent)

URA.5: 12 residues within 4Å: Chain B: H.82, S.83, T.84, G.85, L.114, Y.165, R.168, I.180, S.183, I.184, K.187, F.207 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:L.114, B:I.180, B:F.207 Hydrogen bonds: B:R.168, B:R.168, B:S.183, B:S.183, B:K.187

2 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.6: 4 residues within 4Å: Chain B: K.18, E.22, R.26, Q.64 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.18, B:E.22 Salt bridges: B:R.26 MES.7: 5 residues within 4Å: Chain A: Y.46, F.47, R.48, G.49, R.216 4 PLIP interactions: 4 interactions with chain A Water bridges: A:G.49, A:M.50, A:R.216 Salt bridges: A:R.216

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pugmire, M.J. et al., The crystal structure of pyrimidine nucleoside phosphorylase in a closed conformation. Structure (1998)

Release Date

1999-01-13

Peptides

PROTEIN (PYRIMIDINE NUCLEOSIDE PHOSPHORYLASE): AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

PROTEIN (PYRIMIDINE NUCLEOSIDE PHOSPHORYLASE)