Research workbench
DAB3/HOIP-rbr-LIGAND4
Analyse DAB3/HOIP-rbr-LIGAND4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SC8
- Type
- protein
- Length
- 604 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase RNF31; Single domain antibody
- EC
- 2.3.2.31
- UniProt
- Q96EP0
- Ligands
- L6E, ZN, SO4, CL
- Pockets
- 7 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 25% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase RNF31 (EC 2.3.2.31) | protein | 365 | 37% helix, 11% strand | Q96EP0 |
| B | Single domain antibody | protein | 119 | 5% helix, 52% strand | — |
| C | Single domain antibody | protein | 120 | 10% helix, 51% strand | — |
Ligands and binding sites
- L6E · [2-(methylamino)-2-oxidanylidene-ethyl] (~{E})-4-[(2-oxidanylidene-5,6,7,8-tetrahydro-1~{H}-quinolin-3-yl) carbonylamino]but-2-enoate · ligand · chains A
- ZN · Zinc ion · metal · 8 copies · chains A
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1073 | 0.71 | 0.75 | 94 | L6E, SO4, CL |
| 2 | 65 | 0.71 | 0.97 | 22 | empty |
| 3 | 217 | 0.46 | 0.73 | 30 | empty |
| 4 | 163 | 0.45 | 0.75 | 28 | SO4 |
| 5 | 114 | 0.43 | 0.77 | 26 | CL |
Interfaces
3 interfaces between chains.
- B–C · 969 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 932 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 703 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 1 covalent (disulfide, covalent ligand).
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 Q96EP0
- Elsewhere: RCSB PDB 6SC8 · PDBe 6SC8 · UniProt Q96EP0
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