MolNFT v1 · #90003 · protein + DNA
Damaged DNA induced UV-damaged DNA-binding protein (UV-ddb) dimerization and its roles in chromatinized DNA repair
4E5Z · DNA damage-binding protein 1: “Damaged DNA induced UV-damaged DNA-binding protein (UV-ddb) dimerization and its roles in chromatinized DNA…”. X-ray diffraction, 20 pockets (best druggability 0.86). MolNFT v1 #90003 on GenesisL1: 3D…
- PDB
- 4E5Z
- Type
- protein + DNA
- Length
- 1,590 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA damage-binding protein 1; DNA damage-binding protein 2; AP24 DNA strand; AP24 DNA…
- UniProt
- Q16531, Q92466
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 5% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA damage-binding protein 1 | protein | 1140 | 5% helix, 41% strand | Q16531 |
| B | DNA damage-binding protein 2 | protein | 402 | 5% helix, 31% strand | Q92466 |
| F | AP24 DNA strand | dna | 24 | — | — |
| G | AP24 DNA complementary strand | dna | 24 | — | — |
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1150 | 0.86 | 0.87 | 134 | empty |
| 2 | 981 | 0.82 | 0.83 | 65 | empty |
| 3 | 178 | 0.80 | 0.95 | 28 | empty |
| 4 | 662 | 0.79 | 0.85 | 85 | empty |
| 5 | 615 | 0.79 | 0.84 | 54 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2708 Ų buried · 27 hydrogen bonds · protein-protein
- F–G · 800 Ų buried · 55 hydrogen bonds · nucleic-nucleic
- B–G · 584 Ų buried · 10 hydrogen bonds · protein-nucleic
- B–F · 535 Ų buried · 7 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 disulfide, 1 modified (disulfide, nucleotide modification).
Compared structures
- 4E5Z · Damaged DNA induced UV-damaged DNA-binding protein (UV-DDB) dimerization and its roles in… · the same entry in another collection · chain A against A, TM-score 1.00
- Q92466 · AlphaFold monomer V2.0 prediction for DNA damage-binding protein 2 (Q92466) · a predicted model of the same protein · chain B against A, TM-score 0.97
- Q16531 · AlphaFold monomer V2.0 prediction for DNA damage-binding protein 1 (Q16531) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 Q16531
- Every structure of UniProt Q92466
- Elsewhere: RCSB PDB 4E5Z · PDBe 4E5Z · UniProt Q16531 · UniProt Q92466
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