MolNFT v1 · #127123 · protein
Crystal structure of mindy-1 tmiu in complex with K48-diub
5MN9 · Ubiquitin-40S ribosomal protein S27A: “Crystal structure of mindy-1 tmiu in complex with K48-diub”. X-ray diffraction, 1 pocket (best druggability 0.54). MolNFT v1 #127123 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5MN9
- Type
- protein
- Length
- 168 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin-40S ribosomal protein S27A; Ubiquitin carboxyl-terminal hydrolase mindy-1
- EC
- 3.4.19.12
- UniProt
- P62992, Q8N5J2
- Pockets
- 1 · best druggability 0.54
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin-40S ribosomal protein S27A | protein | 73 | 25% helix, 36% strand | P62992 |
| B | Ubiquitin-40S ribosomal protein S27A | protein | 76 | 24% helix, 34% strand | P62992 |
| C | Ubiquitin carboxyl-terminal hydrolase mindy-1 (EC 3.4.19.12) | protein | 19 | 79% helix, 0% strand | Q8N5J2 |
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 158 | 0.54 | 0.80 | 24 | empty |
Interfaces
3 interfaces between chains.
- A–C · 567 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 274 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 180 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5MN9 · Crystal structure of MINDY-1 tMIU in complex with K48-diUb · the same entry in another collection · chain A against A, TM-score 1.00
- P62992 · AlphaFold monomer V2.0 prediction for ubiquitin-40S ribosomal protein S27A (P62992) · a predicted model of the same protein · chain A against A, TM-score 0.98
- Q8N5J2 · AlphaFold monomer V2.0 prediction for ubiquitin carboxyl-terminal hydrolase mindy-1… · a predicted model of the same protein · chain C against A, TM-score 0.64
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 P62992
- Every structure of UniProt Q8N5J2
- Elsewhere: RCSB PDB 5MN9 · PDBe 5MN9 · UniProt P62992 · UniProt Q8N5J2
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