MolNFT v1 · #78419 · protein

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

3S8I · Protein DDI1 homolog 1: “The retroviral-like protease (rvp) domain of human DDI1”. X-ray diffraction, 2 ligands (PO4, UNX). MolNFT v1 #78419 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3S8I
Type: protein
Length: 245 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein DDI1 homolog 1
UniProt: Q8WTU0
Ligands: PO4, UNX

Structure

x-ray diffraction · 2 distinct chains · 17% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein DDI1 homolog 1	protein	124	17% helix, 44% strand	Q8WTU0
B	Protein DDI1 homolog 1	protein	121	17% helix, 43% strand	Q8WTU0

Ligands and binding sites

PO4 · Phosphate ion · ion · 3 copies · chains A, B
UNX · Unknown atom or ion · ion · chains A, B
EDO · 1,2-ethanediol · additive · chains A
PEG · Di(hydroxyethyl)ether · additive · chains B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Interfaces

1 interface between chains.

A–B · 1264 Å² buried · 22 hydrogen bonds · protein-protein

Compared structures

3S8I · The retroviral-like protease (RVP) domain of human DDI1 · the same entry in another collection · chain B against B, TM-score 1.00
Q8WTU0 · AlphaFold monomer V2.0 prediction for protein DDI1 homolog 1 (Q8WTU0) · a predicted model of the same protein · chain A against A, TM-score 0.98

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q8WTU0
Elsewhere: RCSB PDB 3S8I · PDBe 3S8I · UniProt Q8WTU0

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