Research workbench
Structure of the fanconi anemia id complex bound to icl DNA
Analyse Structure of the fanconi anemia id complex bound to icl DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VAA
- Type
- protein + DNA
- Length
- 2,396 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fanconi anemia, complementation group I; Fanconi anemia group D2 protein; DNA (26-mer)…
- UniProt
- B7ZMF2, Q9BXW9
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 6 distinct chains · 69% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fanconi anemia, complementation group I | protein | 1168 | 69% helix, 1% strand | B7ZMF2 |
| B | Fanconi anemia group D2 protein | protein | 1153 | 68% helix, 2% strand | Q9BXW9 |
| W | DNA (26-mer) | dna | 26 | — | — |
| X | DNA (5'- D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3') | dna | 18 | — | — |
| Y | DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)- 3') | dna | 15 | — | — |
| Z | DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)- 3') | dna | 16 | — | — |
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1184 | 0.81 | 0.82 | 121 | empty |
| 2 | 1133 | 0.77 | 0.79 | 90 | empty |
| 3 | 161 | 0.75 | 0.92 | 29 | empty |
| 4 | 506 | 0.73 | 0.82 | 47 | empty |
| 5 | 409 | 0.70 | 0.82 | 57 | empty |
Interfaces
8 interfaces between chains.
- A–B · 2545 Ų buried · 24 hydrogen bonds · protein-protein
- W–X · 868 Ų buried · 39 hydrogen bonds · nucleic-nucleic
- Y–Z · 634 Ų buried · 30 hydrogen bonds · nucleic-nucleic
- B–Y · 397 Ų buried · 6 hydrogen bonds · protein-nucleic
- B–Z · 273 Ų buried · 2 hydrogen bonds · protein-nucleic
Compared structures
- 6VAA · Structure of the Fanconi Anemia ID complex bound to ICL DNA · the same entry in another collection · chain W against W, 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 0.85
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
- Elsewhere: RCSB PDB 6VAA · PDBe 6VAA · UniProt B7ZMF2 · UniProt Q9BXW9
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