MolNFT v1 · #156380 · protein
Distinct mechanism of MUL1-ring domain simultaneously recruiting E2 enzyme and the substrate P53-tad domain
6M2C · Ubiquitin-conjugating enzyme E2 D2: “Distinct mechanism of MUL1-ring domain simultaneously recruiting E2 enzyme and the substrate P53-tad domain”. X-ray diffraction, 1 ligand (ZN), 11 pockets (best druggability 0.78). MolNFT v1…
- PDB
- 6M2C
- Type
- protein
- Length
- 816 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin-conjugating enzyme E2 D2; Mitochondrial ubiquitin ligase activator of nfkb 1
- EC
- 2.3.2.23, 2.3.2.24, 2.3.2.27
- UniProt
- P62837, Q969V5
- Ligands
- ZN
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Ubiquitin-conjugating enzyme E2 D2 (EC 2.3.2.23, 2.3.2.24) | protein | 149 | 38% helix, 17% strand | P62837 |
| E, F, G, H | Mitochondrial ubiquitin ligase activator of nfkb 1 (EC 2.3.2.27) | protein | 55 | 11% helix, 29% strand | Q969V5 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1128 | 0.78 | 0.80 | 91 | empty |
| 2 | 831 | 0.74 | 0.78 | 76 | empty |
| 3 | 433 | 0.59 | 0.75 | 54 | empty |
| 4 | 112 | 0.43 | 0.77 | 18 | empty |
| 5 | 97 | 0.42 | 0.77 | 17 | empty |
Interfaces
12 interfaces between chains.
- D–H · 562 Ų buried · 6 hydrogen bonds · protein-protein
- A–E · 498 Ų buried · 6 hydrogen bonds · protein-protein
- B–F · 494 Ų buried · 5 hydrogen bonds · protein-protein
- C–G · 487 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 346 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6M2C · Distinct mechanism of MUL1-RING domain simultaneously recruiting E2 enzyme and the… · the same entry in another collection · chain H against H, TM-score 1.00
- P62837 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 D2 (P62837) · a predicted model of the same protein · chain A against A, TM-score 0.98
- Q969V5 · AlphaFold monomer V2.0 prediction for mitochondrial ubiquitin ligase activator of nfkb 1… · a predicted model of the same protein · chain E against A, TM-score 0.92
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 Q969V5
- Elsewhere: RCSB PDB 6M2C · PDBe 6M2C · UniProt P62837 · UniProt Q969V5
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