MolNFT v1 · #27215 · protein

Crystal structure of UCHL3-ubvme complex

1XD3 · Ubiquitin carboxyl-terminal esterase L3: “Crystal structure of UCHL3-ubvme complex”. X-ray diffraction, 2 ligands (GVE, MG), 5 pockets (best druggability 0.63). MolNFT v1 #27215 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 1XD3
Type: protein
Length: 606 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ubiquitin carboxyl-terminal esterase L3; Ubc protein
EC: 3.4.19.12
UniProt: P15374, P62988
Ligands: GVE, MG
Pockets: 5 · best druggability 0.63

Structure

x-ray diffraction · 3 distinct chains · 36% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ubiquitin carboxyl-terminal esterase L3 (EC 3.4.19.12)	protein	229	39% helix, 20% strand	P15374
B, D	Ubc protein	protein	75	20% helix, 36% strand	P62988
C	Ubiquitin carboxyl-terminal esterase L3 (EC 3.4.19.12)	protein	227	39% helix, 20% strand	P15374

Ligands and binding sites

GVE · Methyl 4-aminobutanoate · ligand · 2 copies · chains A, B, C, D
MG · Magnesium ion · metal · 10 copies · chains A, C

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	528	0.63	0.75	64	empty
2	87	0.41	0.78	15	empty
3	78	0.34	0.75	14	empty
4	64	0.30	0.74	17	empty
5	56	0.27	0.74	12	empty

Interfaces

5 interfaces between chains.

A–B · 1181 Å² buried · 17 hydrogen bonds · protein-protein
C–D · 1125 Å² buried · 15 hydrogen bonds · protein-protein
A–D · 136 Å² buried · 2 hydrogen bonds · protein-protein
B–C · 134 Å² buried · 0 hydrogen bonds · protein-protein
A–C · 62 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 4 covalent (covalent ligand).

Compared structures

1XD3 · Crystal structure of UCHL3-UbVME complex · the same entry in another collection · chain D against D, TM-score 1.00
P15374 · AlphaFold monomer V2.0 prediction for ubiquitin carboxyl-terminal hydrolase isozyme L3… · a predicted model of the same protein · chain C against A, TM-score 0.99

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 P15374
Every structure of UniProt P62988
Elsewhere: RCSB PDB 1XD3 · PDBe 1XD3 · UniProt P15374 · UniProt P62988

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