MolNFT v1 · #137364 · protein
Crystal structure of ubr-box from UBR6 in a domain-swapping conformation
5VMD · F-box only protein 11: “Crystal structure of ubr-box from UBR6 in a domain-swapping conformation”. X-ray diffraction, 1 ligand (ZN), 3 pockets (best druggability 0.47). MolNFT v1 #137364 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5VMD
- Type
- protein
- Length
- 280 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- F-box only protein 11
- UniProt
- Q86XK2
- Ligands
- ZN
- Pockets
- 3 · best druggability 0.47
Structure
x-ray diffraction · 4 distinct chains · 22% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | F-box only protein 11 | protein | 69 | 25% helix, 22% strand | Q86XK2 |
| B | F-box only protein 11 | protein | 72 | 22% helix, 21% strand | Q86XK2 |
| C | F-box only protein 11 | protein | 73 | 16% helix, 21% strand | Q86XK2 |
| D | F-box only protein 11 | protein | 66 | 24% helix, 23% strand | Q86XK2 |
Ligands and binding sites
- ZN · Zinc ion · metal · 14 copies · chains A, C, B, D
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 140 | 0.47 | 0.77 | 28 | EDO |
| 2 | 111 | 0.42 | 0.76 | 27 | EDO |
| 3 | 57 | 0.33 | 0.77 | 11 | EDO |
Interfaces
4 interfaces between chains.
- A–C · 1293 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 1272 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 254 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 90 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5VMD · Crystal structure of UBR-box from UBR6 in a domain-swapping conformation · the same entry in another collection · chain D against D, TM-score 1.00
- Q86XK2 · AlphaFold monomer V2.0 prediction for F-box only protein 11 (Q86XK2) · a predicted model of the same protein · chain D against A, TM-score 0.48
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 Q86XK2
- Elsewhere: RCSB PDB 5VMD · PDBe 5VMD · UniProt Q86XK2
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