SMTL ID : 3djo.1

Bovine Seminal Ribonuclease uridine 2' phosphate complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

2 x U2P: PHOSPHORIC ACID MONO-[2-(2,4-DIOXO-3,4-DIHYDRO-2H-PYRIMIDIN-1-YL)-4-HYDROXY-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-3-YL] ESTER(Non-covalent)

U2P.1: 9 residues within 4Å: Chain A: V.43, N.44, T.45, K.66, R.85, F.120, D.121, A.122 Chain B: H.12 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:T.45, A:T.45, A:T.45, A:S.123 Water bridges: A:K.66, A:K.66, A:K.66, A:K.66, A:R.85, A:R.85, A:R.85 Salt bridges: A:K.66, A:R.85 U2P.2: 10 residues within 4Å: Chain A: Q.11, H.12 Chain B: K.41, V.43, N.44, T.45, H.119, F.120, D.121, A.122 12 PLIP interactions: 2 interactions with chain A, 10 interactions with chain B Hydrogen bonds: A:Q.11, B:T.45, B:T.45, B:T.45, B:F.120, B:F.120 Salt bridges: A:H.12, B:K.41, B:H.119 Water bridges: B:D.121, B:S.123, B:S.123

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 5 residues within 4Å: Chain A: K.41, H.119, F.120 Chain B: Q.11, H.12 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:F.120 Salt bridges: A:K.41, A:H.119, B:H.12 ACT.4: 4 residues within 4Å: Chain A: N.27 Chain B: M.29, C.32, R.33 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.27 Salt bridges: B:R.33

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dossi, K. et al., Mapping the ribonucleolytic active site of bovine seminal ribonuclease. The binding of pyrimidinyl phosphonucleotide inhibitors. Eur.J.Med.Chem. (2009)

Release Date

2009-06-30

Peptides

Seminal ribonuclease: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Seminal ribonuclease

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