MolNFT v1 · #156182 · protein
USP14 catalytic domain mutant C114S
6LVS · Ubiquitin carboxyl-terminal hydrolase 14: “USP14 catalytic domain mutant C114S”. X-ray diffraction, 1 ligand (NA), 20 pockets (best druggability 0.82). MolNFT v1 #156182 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6LVS
- Type
- protein
- Length
- 1,982 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin carboxyl-terminal hydrolase 14
- EC
- 3.4.19.12
- UniProt
- P54578
- Ligands
- NA
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 6 distinct chains · 29% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin carboxyl-terminal hydrolase 14 (EC 3.4.19.12) | protein | 331 | 29% helix, 34% strand | P54578 |
| B | Ubiquitin carboxyl-terminal hydrolase 14 (EC 3.4.19.12) | protein | 330 | 29% helix, 33% strand | P54578 |
| C | Ubiquitin carboxyl-terminal hydrolase 14 (EC 3.4.19.12) | protein | 333 | 31% helix, 32% strand | P54578 |
| D | Ubiquitin carboxyl-terminal hydrolase 14 (EC 3.4.19.12) | protein | 329 | 31% helix, 32% strand | P54578 |
| E | Ubiquitin carboxyl-terminal hydrolase 14 (EC 3.4.19.12) | protein | 328 | 28% helix, 31% strand | P54578 |
| F | Ubiquitin carboxyl-terminal hydrolase 14 (EC 3.4.19.12) | protein | 331 | 28% helix, 30% strand | P54578 |
Ligands and binding sites
- NA · Sodium ion · metal · 41 copies · chains A, B, C, D, E, F
- FMT · Formic acid · additive · 26 copies · chains A, B, C, D, E, F
- GOL · Glycerol · additive · 12 copies · chains A, C, B, D, E
- BME · Beta-mercaptoethanol · additive · 9 copies · chains A, B, C, E, F
- EDO · 1,2-ethanediol · additive · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1004 | 0.82 | 0.83 | 98 | BME |
| 2 | 745 | 0.78 | 0.82 | 71 | GOL, NA, FMT |
| 3 | 475 | 0.62 | 0.76 | 48 | FMT |
| 4 | 480 | 0.62 | 0.75 | 48 | empty |
| 5 | 298 | 0.56 | 0.76 | 35 | empty |
Interfaces
9 interfaces between chains.
- A–C · 1184 Ų buried · 16 hydrogen bonds · protein-protein
- A–F · 536 Ų buried · 6 hydrogen bonds · protein-protein
- E–F · 381 Ų buried · 1 hydrogen bond · protein-protein
- C–E · 377 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 315 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
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 P54578
- Elsewhere: RCSB PDB 6LVS · PDBe 6LVS · UniProt P54578
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