MolNFT v1 · #167090 · protein + DNA
Structure of mono-ubiquitinated FANCD2 bound to non-ubiquitinated fanci and to DNA
6VAF · Fanconi anemia, complementation group I: “Structure of mono-ubiquitinated FANCD2 bound to non-ubiquitinated fanci and to DNA”. Electron microscopy, 20 pockets (best druggability 0.75). MolNFT v1 #167090 on GenesisL1: 3D structure…
- PDB
- 6VAF
- Type
- protein + DNA
- Length
- 2,487 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fanconi anemia, complementation group I; Fanconi anemia group D2 protein; Ubiquitin; DNA…
- UniProt
- B7ZMF2, Q9BXW9, P0CG48
- Pockets
- 20 · best druggability 0.75
Structure
electron microscopy · 5 distinct chains · 66% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fanconi anemia, complementation group I | protein | 1198 | 71% helix, 1% strand | B7ZMF2 |
| B | Fanconi anemia group D2 protein | protein | 1155 | 65% helix, 2% strand | Q9BXW9 |
| D | Ubiquitin | protein | 76 | 14% helix, 32% strand | P0CG48 |
| S | DNA (29-mer) | dna | 29 | — | — |
| T | DNA (29-mer) | dna | 29 | — | — |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 75 | 0.75 | 0.98 | 19 | empty |
| 2 | 1004 | 0.72 | 0.76 | 89 | empty |
| 3 | 86 | 0.72 | 0.94 | 32 | empty |
| 4 | 707 | 0.70 | 0.77 | 72 | empty |
| 5 | 83 | 0.69 | 0.93 | 21 | empty |
Interfaces
8 interfaces between chains.
- A–B · 3760 Ų buried · 34 hydrogen bonds · protein-protein
- S–T · 1357 Ų buried · 110 hydrogen bonds · nucleic-nucleic
- A–D · 751 Ų buried · 7 hydrogen bonds · protein-protein
- A–S · 414 Ų buried · 9 hydrogen bonds · protein-nucleic
- B–D · 327 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6VAF · Structure of mono-ubiquitinated FANCD2 bound to non-ubiquitinated FANCI and to DNA · the same entry in another collection · chain T against T, TM-score 1.00
- Q9BXW9 · AlphaFold monomer V2.0 prediction for fanconi anemia group D2 protein (Q9BXW9) · a predicted model of the same protein · chain B against A, TM-score 0.76
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 B7ZMF2
- Every structure of UniProt Q9BXW9
- Every structure of UniProt P0CG48
- Elsewhere: RCSB PDB 6VAF · PDBe 6VAF · UniProt B7ZMF2 · UniProt Q9BXW9 · UniProt P0CG48
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.