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Crystal structure of UPLC1 gap domain
Analyse Crystal structure of UPLC1 gap domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2B0O
- Type
- protein
- Length
- 1,045 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- UPLC1
- UniProt
- Q6P9F4
- Ligands
- ZN
- Pockets
- 16 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | UPLC1 | protein | 264 | 46% helix, 6% strand | Q6P9F4 |
| F | UPLC1 | protein | 266 | 48% helix, 5% strand | Q6P9F4 |
| G | UPLC1 | protein | 253 | 51% helix, 5% strand | Q6P9F4 |
| H | UPLC1 | protein | 262 | 46% helix, 5% strand | Q6P9F4 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 918 | 0.85 | 0.87 | 76 | empty |
| 2 | 150 | 0.77 | 0.95 | 24 | empty |
| 3 | 675 | 0.74 | 0.80 | 57 | empty |
| 4 | 429 | 0.67 | 0.80 | 46 | empty |
| 5 | 200 | 0.67 | 0.85 | 26 | empty |
Interfaces
6 interfaces between chains.
- E–F · 2448 Ų buried · 27 hydrogen bonds · protein-protein
- G–H · 2266 Ų buried · 21 hydrogen bonds · protein-protein
- E–G · 409 Ų buried · 3 hydrogen bonds · protein-protein
- F–H · 344 Ų buried · 5 hydrogen bonds · protein-protein
- F–G · 270 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2B0O · Crystal structure of UPLC1 GAP domain · the same entry in another collection · chain E against E, TM-score 1.00
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 Q6P9F4
- Elsewhere: RCSB PDB 2B0O · PDBe 2B0O · UniProt Q6P9F4
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