Research workbench
Structure of monoubiquitinated FANCD2 in complex with fanci and DNA
Analyse Structure of monoubiquitinated FANCD2 in complex with fanci and DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TNF
- Type
- protein + DNA
- Length
- 2,272 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- FANCD2; Fanconi anemia complementation group I; Polyubiquitin-C; DNA (33-mer)
- UniProt
- F1NP22, B0I564, P0CG48
- Pockets
- 19 · best druggability 0.72
Structure
electron microscopy · 4 distinct chains · 57% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | FANCD2 | protein | 1116 | 57% helix, 1% strand | F1NP22 |
| B | Fanconi anemia complementation group I | protein | 1014 | 61% helix, 0% strand | B0I564 |
| C | Polyubiquitin-C | protein | 76 | 12% helix, 11% strand | P0CG48 |
| D, E | DNA (33-mer) | dna | 33 | — | — |
Pockets
19 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1130 | 0.72 | 0.76 | 161 | empty |
| 2 | 525 | 0.64 | 0.77 | 82 | empty |
| 3 | 574 | 0.64 | 0.76 | 103 | empty |
| 4 | 488 | 0.62 | 0.76 | 81 | empty |
| 5 | 651 | 0.61 | 0.73 | 89 | empty |
Interfaces
7 interfaces between chains.
- A–B · 270 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 268 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 136 Ų buried · 1 hydrogen bond · protein-protein
- D–E · 136 Ų buried · 2 hydrogen bonds · nucleic-nucleic
- A–D · 18 Ų buried · 0 hydrogen bonds · protein-nucleic
Compared structures
- 6TNF · Structure of monoubiquitinated FANCD2 in complex with FANCI and DNA · the same entry in another collection · chain E against E, 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 F1NP22
- Every structure of UniProt B0I564
- Every structure of UniProt P0CG48
- Elsewhere: RCSB PDB 6TNF · PDBe 6TNF · UniProt F1NP22 · UniProt B0I564 · UniProt P0CG48
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