Research workbench
Crystal structure of FAAP20 ubz domain in complex with LYS63-linked diubiquitin
Analyse Crystal structure of FAAP20 ubz domain in complex with LYS63-linked diubiquitin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WWQ
- Type
- protein
- Length
- 759 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin; Fanconi anemia-associated protein of 20 kda
- UniProt
- P0CG50, Q6NZ36
- Ligands
- ZN
- Pockets
- 6 · best druggability 0.51
Structure
x-ray diffraction · 6 distinct chains · 27% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G, J | Ubiquitin | protein | 76 | 24% helix, 34% strand | P0CG50 |
| B, E, K | Ubiquitin | protein | 76 | 20% helix, 34% strand | P0CG50 |
| C, I | Fanconi anemia-associated protein of 20 kda | protein | 38 | 37% helix, 5% strand | Q6NZ36 |
| F | Fanconi anemia-associated protein of 20 kda | protein | 39 | 36% helix, 5% strand | Q6NZ36 |
| H | Ubiquitin | protein | 75 | 24% helix, 35% strand | P0CG50 |
| L | Fanconi anemia-associated protein of 20 kda | protein | 37 | 38% helix, 5% strand | Q6NZ36 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains C, F, I, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 133 | 0.51 | 0.80 | 23 | empty |
| 2 | 144 | 0.50 | 0.79 | 23 | empty |
| 3 | 107 | 0.42 | 0.77 | 19 | empty |
| 4 | 93 | 0.40 | 0.77 | 19 | empty |
| 5 | 91 | 0.37 | 0.76 | 12 | empty |
Interfaces
20 interfaces between chains.
- E–J · 715 Ų buried · 11 hydrogen bonds · protein-protein
- D–K · 697 Ų buried · 8 hydrogen bonds · protein-protein
- A–H · 684 Ų buried · 7 hydrogen bonds · protein-protein
- B–G · 683 Ų buried · 7 hydrogen bonds · protein-protein
- D–F · 667 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 isopeptide (isopeptide).
Compared structures
- 3WWQ · Crystal structure of FAAP20 UBZ domain in complex with Lys63-linked diubiquitin · the same entry in another collection · chain L against L, 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 P0CG50
- Every structure of UniProt Q6NZ36
- Elsewhere: RCSB PDB 3WWQ · PDBe 3WWQ · UniProt P0CG50 · UniProt Q6NZ36
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