Research workbench
Crystal structure of yeast proteasome interacting protein
Analyse Crystal structure of yeast proteasome interacting protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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.
| Volume (ų) | 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 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 993 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 477 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 347 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 23 Ų 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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