MolNFT v1 · #116039 · protein

Crystal structure of UBCH5B in complex with the ring-U5BR fragment of AO7 (Y165A)

5D1L · Ubiquitin-conjugating enzyme E2 D2: “Crystal structure of UBCH5B in complex with the ring-U5BR fragment of AO7 (Y165A)”. X-ray diffraction, 2 ligands (OXL, ZN), 4 pockets (best druggability 0.53). MolNFT v1 #116039 on GenesisL1: 3D…

PDB: 5D1L
Type: protein
Length: 257 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ubiquitin-conjugating enzyme E2 D2; E3 ubiquitin-protein ligase RNF25
EC: 6.3.2.19, 6.3.2.-
UniProt: P62837, Q96BH1
Ligands: OXL, ZN
Pockets: 4 · best druggability 0.53

Structure

x-ray diffraction · 2 distinct chains · 37% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ubiquitin-conjugating enzyme E2 D2 (EC 6.3.2.19)	protein	146	36% helix, 21% strand	P62837
B	E3 ubiquitin-protein ligase RNF25 (EC 6.3.2.-)	protein	111	39% helix, 10% strand	Q96BH1

Ligands and binding sites

OXL · Oxalate ion · ligand · chains A
ZN · Zinc ion · metal · 2 copies · chains B
PEG · Di(hydroxyethyl)ether · additive · chains A

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

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	87	0.53	0.84	17	empty
2	133	0.50	0.80	22	empty
3	175	0.49	0.77	27	empty
4	54	0.28	0.75	14	empty

Interfaces

1 interface between chains.

A–B · 1582 Å² buried · 20 hydrogen bonds · protein-protein

Compared structures

5D1L · Crystal Structure of UbcH5B in Complex with the RING-U5BR Fragment of AO7 (Y165A) · the same entry in another collection · chain A against A, TM-score 1.00
P62837 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 D2 (P62837) · a predicted model of the same protein · chain A against A, TM-score 0.98
Q96BH1 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase RNF25 (Q96BH1) · a predicted model of the same protein · chain B against A, TM-score 0.84

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 P62837
Every structure of UniProt Q96BH1
Elsewhere: RCSB PDB 5D1L · PDBe 5D1L · UniProt P62837 · UniProt Q96BH1

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