Research workbench
Structure of the human fanconi anaemia Core-UBE2T-ID-DNA complex in intermediate state
Analyse Structure of the human fanconi anaemia Core-UBE2T-ID-DNA complex in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KZT
- Type
- protein + DNA
- Length
- 11,045 residues
- Chains
- 19
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 4.2
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- Fanconi anemia group A protein; Fanconi anemia group B protein; Fanconi anemia group C…
- EC
- 2.3.2.27, 2.3.2.23
- UniProt
- O15360, Q8NB91, Q00597, Q9HB96, Q9NPI8, O15287, Q9NW38, Q0VG06, Q9NPD8, B7ZMF2, Q9BXW9
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · resolution 4.2 · 18 distinct chains · 54% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fanconi anemia group A protein | protein | 1186 | 68% helix, 0% strand | O15360 |
| B | Fanconi anemia group B protein | protein | 701 | 22% helix, 35% strand | Q8NB91 |
| C | Fanconi anemia group C protein | protein | 550 | 70% helix, 0% strand | Q00597 |
| E | Fanconi anemia group E protein | protein | 419 | 61% helix, 2% strand | Q9HB96 |
| F | Fanconi anemia group F protein | protein | 340 | 68% helix, 3% strand | Q9NPI8 |
| G | Fanconi anemia group G protein | protein | 577 | 69% helix, 0% strand | O15287 |
| H | Fanconi anemia group G protein | protein | 544 | 71% helix, 0% strand | O15287 |
| L, M | E3 ubiquitin-protein ligase FANCL (EC 2.3.2.27) | protein | 370 | 30% helix, 19% strand | Q9NW38 |
| O | Fanconi anemia group B protein | protein | 699 | 20% helix, 35% strand | Q8NB91 |
| P | Fanconi anemia core complex-associated protein 100 | protein | 748 | 23% helix, 31% strand | Q0VG06 |
| Q | Fanconi anemia core complex-associated protein 100 | protein | 754 | 21% helix, 31% strand | Q0VG06 |
| S | Fanconi anemia group A protein | protein | 1250 | 68% helix, 0% strand | O15360 |
| W | Fanconi anemia core complex-associated protein 20 | protein | 39 | 0% helix, 10% strand | — |
| X | Ubiquitin-conjugating enzyme E2 T (EC 2.3.2.23) | protein | 153 | 36% helix, 16% strand | Q9NPD8 |
| U | Fanconi anemia, complementation group I | protein | 1181 | 71% helix, 1% strand | B7ZMF2 |
| V | Fanconi anemia group D2 protein | protein | 1120 | 69% helix, 2% strand | Q9BXW9 |
| Y | DNA (22-mer) | dna | 22 | — | — |
| Z | DNA (22-mer) | dna | 22 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 5 copies · chains G, L, M
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 826 | 0.84 | 0.87 | 77 | empty |
| 2 | 1188 | 0.83 | 0.84 | 118 | empty |
| 3 | 1078 | 0.82 | 0.84 | 100 | empty |
| 4 | 1112 | 0.82 | 0.83 | 112 | empty |
| 5 | 1037 | 0.82 | 0.82 | 81 | empty |
Interfaces
41 interfaces between chains.
- B–P · 7482 Ų buried · 67 hydrogen bonds · protein-protein
- O–Q · 7448 Ų buried · 68 hydrogen bonds · protein-protein
- C–F · 3135 Ų buried · 23 hydrogen bonds · protein-protein
- C–E · 2953 Ų buried · 24 hydrogen bonds · protein-protein
- A–H · 2590 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- Q9NPD8 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 T (Q9NPD8) · a predicted model of the same protein · chain X against A, TM-score 0.96
- O15287 · AlphaFold monomer V2.0 prediction for fanconi anemia group G protein (O15287) · a predicted model of the same protein · chain H against A, TM-score 0.92
- Q00597 · AlphaFold monomer V2.0 prediction for fanconi anemia group C protein (Q00597) · a predicted model of the same protein · chain C against A, TM-score 0.88
- Q9BXW9 · AlphaFold monomer V2.0 prediction for fanconi anemia group D2 protein (Q9BXW9) · a predicted model of the same protein · chain V against A, TM-score 0.81
- O15360 · AlphaFold monomer V2.0 prediction for fanconi anemia group a protein (O15360) · a predicted model of the same protein · chain S against A, TM-score 0.75
- Q9NW38 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase fancl (Q9NW38) · a predicted model of the same protein · chain M against A, TM-score 0.71
- Q9NPI8 · AlphaFold monomer V2.0 prediction for fanconi anemia group F protein (Q9NPI8) · a predicted model of the same protein · chain F against A, TM-score 0.64
- Q0VG06 · AlphaFold monomer V2.0 prediction for fanconi anemia core complex- associated protein 100… · a predicted model of the same protein · chain P against A, TM-score 0.61
- Q9HB96 · AlphaFold monomer V2.0 prediction for fanconi anemia group E protein (Q9HB96) · a predicted model of the same protein · chain E against A, TM-score 0.58
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 O15360
- Every structure of UniProt Q8NB91
- Every structure of UniProt Q00597
- Every structure of UniProt Q9HB96
- Every structure of UniProt Q9NPI8
- Every structure of UniProt O15287
- Every structure of UniProt Q9NW38
- Every structure of UniProt Q0VG06
- Every structure of UniProt Q9NPD8
- Every structure of UniProt B7ZMF2
- Every structure of UniProt Q9BXW9
- Elsewhere: RCSB PDB 7KZT · PDBe 7KZT · UniProt O15360 · UniProt Q8NB91 · UniProt Q00597 · UniProt Q9HB96 · UniProt Q9NPI8 · UniProt O15287 · UniProt Q9NW38 · UniProt Q0VG06 · UniProt Q9NPD8 · UniProt B7ZMF2 · UniProt Q9BXW9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.