SMTL ID : 3s8i.1

The retroviral-like protease (RVP) domain of human DDI1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

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

PO4.1: 4 residues within 4Å: Chain A: R.82, H.84, S.98 Chain B: G.2 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:G.2, A:S.98 Water bridges: A:S.98 Salt bridges: A:R.82, A:H.84 PO4.5: 3 residues within 4Å: Chain B: R.82, H.84, S.98 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.98, B:S.98 Salt bridges: B:R.82, B:H.84 PO4.6: 2 residues within 4Å: Chain B: H.34, R.56 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:H.34, B:R.56

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 5 residues within 4Å: Chain A: N.28, C.29, K.30, Q.89, E.91 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:C.29, A:Q.89, A:E.91 Water bridges: A:E.91, A:E.91, A:T.139

1 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.3: 4 residues within 4Å: Chain A: D.41, G.43 Chain B: D.41, G.43 No protein-ligand interaction detected (PLIP)

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 7 residues within 4Å: Chain B: N.28, C.29, K.30, P.35, L.36, Q.89, E.91 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.28, B:C.29, B:L.36, B:L.36, B:E.91 Water bridges: B:E.91

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Walker, J.R. et al., Retropepsin-Like Domain of Human DDI1. To be Published

Release Date

2011-07-06

Peptides

Protein DDI1 homolog 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Protein DDI1 homolog 1