MolNFT v1 · #168223 · protein
RNF12 ring domain in complex with a UBE2D2~UB conjugate
6W9D · Ubiquitin-conjugating enzyme E2 D2: “RNF12 ring domain in complex with a UBE2D2~UB conjugate”. X-ray diffraction, 2 ligands (ZN, IOD), 9 pockets (best druggability 0.67). MolNFT v1 #168223 on GenesisL1: 3D structure, binding sites…
- PDB
- 6W9D
- Type
- protein
- Length
- 854 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin-conjugating enzyme E2 D2; E3 ubiquitin-protein ligase rlim; Ubiquitin
- EC
- 2.3.2.23, 2.3.2.24, 2.3.2.27
- UniProt
- P62837, Q9NVW2, P0CG48
- Ligands
- ZN, IOD
- Pockets
- 9 · best druggability 0.67
Structure
x-ray diffraction · 6 distinct chains · 29% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Ubiquitin-conjugating enzyme E2 D2 (EC 2.3.2.23, 2.3.2.24) | protein | 148 | 36% helix, 18% strand | P62837 |
| B | E3 ubiquitin-protein ligase rlim (EC 2.3.2.27) | protein | 62 | 19% helix, 21% strand | Q9NVW2 |
| C, I | Ubiquitin | protein | 72 | 25% helix, 33% strand | P0CG48 |
| E, H | E3 ubiquitin-protein ligase rlim (EC 2.3.2.27) | protein | 67 | 18% helix, 22% strand | Q9NVW2 |
| F | Ubiquitin | protein | 70 | 27% helix, 31% strand | P0CG48 |
| G | Ubiquitin-conjugating enzyme E2 D2 (EC 2.3.2.23, 2.3.2.24) | protein | 148 | 36% helix, 18% strand | P62837 |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains B, E, H
- IOD · Iodide ion · ion · 8 copies · chains B, C, D, E, F, G, H, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 552 | 0.67 | 0.78 | 63 | IOD |
| 2 | 168 | 0.60 | 0.83 | 34 | IOD |
| 3 | 172 | 0.60 | 0.82 | 33 | IOD |
| 4 | 329 | 0.57 | 0.76 | 51 | empty |
| 5 | 269 | 0.54 | 0.76 | 46 | empty |
Interfaces
12 interfaces between chains.
- G–H · 631 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 610 Ų buried · 5 hydrogen bonds · protein-protein
- D–E · 599 Ų buried · 4 hydrogen bonds · protein-protein
- G–I · 594 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 584 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 P62837
- Every structure of UniProt Q9NVW2
- Every structure of UniProt P0CG48
- Elsewhere: RCSB PDB 6W9D · PDBe 6W9D · UniProt P62837 · UniProt Q9NVW2 · UniProt P0CG48
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