MolNFT v1 · #82388 · protein

Crystal structure of yeast proteasome interacting protein

3VLD · DNA mismatch repair protein HSM3: “Crystal structure of yeast proteasome interacting protein”. X-ray diffraction, 5 pockets (best druggability 0.66). MolNFT v1 #82388 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3VLD
Type: protein
Length: 914 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA mismatch repair protein HSM3
UniProt: P38348
Pockets: 5 · best druggability 0.66

Structure

x-ray diffraction · 1 distinct chain · 73% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	DNA mismatch repair protein HSM3	protein	457	73% helix, 0% strand	P38348

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	307	0.66	0.81	40	empty
2	182	0.64	0.84	33	empty
3	284	0.55	0.76	32	empty
4	286	0.55	0.76	35	empty
5	87	0.35	0.75	18	empty

Interfaces

1 interface between chains.

A–B · 1765 Å² buried · 21 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 modified (engineered).

Compared structures

3VLD · Crystal structure of yeast proteasome interacting protein · the same entry in another collection · chain A against A, TM-score 1.00
P38348 · AlphaFold monomer V2.0 prediction for DNA mismatch repair protein HSM3 (P38348) · a predicted model of the same protein · chain A against A, TM-score 0.95

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 P38348
Elsewhere: RCSB PDB 3VLD · PDBe 3VLD · UniProt P38348

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