MolNFT v1 · #82390 · protein

Crystal structure of yeast proteasome interacting protein

3VLF · DNA mismatch repair protein HSM3: “Crystal structure of yeast proteasome interacting protein”. X-ray diffraction, 9 pockets (best druggability 0.78). MolNFT v1 #82390 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3VLF
Type: protein
Length: 1,057 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA mismatch repair protein HSM3; 26S protease regulatory subunit 7 homolog
UniProt: P38348, P33299
Pockets: 9 · best druggability 0.78

Structure

x-ray diffraction · 3 distinct chains · 64% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA mismatch repair protein HSM3	protein	457	66% helix, 0% strand	P38348
B, D	26S protease regulatory subunit 7 homolog	protein	73	62% helix, 3% strand	P33299
C	DNA mismatch repair protein HSM3	protein	454	63% helix, 0% strand	P38348

Pockets

9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	136	0.78	0.95	25	empty
2	85	0.71	0.95	27	empty
3	74	0.65	0.92	22	empty
4	309	0.64	0.80	39	empty
5	341	0.61	0.78	33	empty

Interfaces

5 interfaces between chains.

A–B · 1001 Å² buried · 14 hydrogen bonds · protein-protein
C–D · 993 Å² buried · 13 hydrogen bonds · protein-protein
B–C · 477 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 347 Å² buried · 2 hydrogen bonds · protein-protein
A–D · 23 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 22 modified (engineered).

Compared structures

3VLF · 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
P33299 · AlphaFold monomer V2.0 prediction for 26S proteasome regulatory subunit 7 homolog (P33299) · a predicted model of the same protein · chain B against A, TM-score 0.94

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
Every structure of UniProt P33299
Elsewhere: RCSB PDB 3VLF · PDBe 3VLF · UniProt P38348 · UniProt P33299

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