SMTL ID : 11ba.1

BINDING OF A SUBSTRATE ANALOGUE TO A DOMAIN SWAPPING PROTEIN IN THE COMPLEX OF BOVINE SEMINAL RIBONUCLEASE WITH URIDYLYL-2',5'-ADENOSINE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.06 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: N.67, H.119, D.121 Ligands: UPA.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.67 Salt bridges: A:H.119 SO4.3: 4 residues within 4Å: Chain B: N.67, H.119, D.121 Ligands: UPA.5 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.67 Salt bridges: B:H.119 SO4.4: 2 residues within 4Å: Chain B: G.16, N.17 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.17, B:N.17

2 x UPA: URIDYLYL-2'-5'-PHOSPHO-ADENOSINE(Non-covalent)

UPA.2: 18 residues within 4Å: Chain A: K.41, V.43, N.44, T.45, C.65, N.67, Q.69, N.71, A.109, V.118, H.119, F.120, D.121, A.122 Chain B: K.7, Q.11, H.12 Ligands: SO4.1 15 PLIP interactions: 13 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:T.45, A:T.45, A:T.45, A:N.67, A:N.71, A:N.71, A:H.119, A:F.120, A:F.120, B:Q.11 Water bridges: A:S.123 Salt bridges: A:K.41, A:H.119, B:H.12 pi-Stacking: A:H.119 UPA.5: 17 residues within 4Å: Chain A: Q.11, H.12 Chain B: K.41, V.43, N.44, T.45, C.65, N.67, Q.69, N.71, A.109, V.118, H.119, F.120, D.121, A.122 Ligands: SO4.3 14 PLIP interactions: 11 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:T.45, B:T.45, B:T.45, B:N.67, B:N.71, B:N.71, B:F.120 Water bridges: B:S.123, A:Q.11, A:Q.11 Salt bridges: B:K.41, B:H.119, A:H.12 pi-Stacking: B:H.119

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vitagliano, L. et al., Binding of a substrate analog to a domain swapping protein: X-ray structure of the complex of bovine seminal ribonuclease with uridylyl(2',5')adenosine. Protein Sci. (1998)

Release Date

1999-03-26

Peptides

PROTEIN (RIBONUCLEASE, SEMINAL): AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

PROTEIN (RIBONUCLEASE, SEMINAL)

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