MolNFT v1 · #85049 · protein + DNA
Structure of HSDDB1-DRDDB2 bound to a 16 bp cpd-duplex (pyrimidine at D-1 position) at 3.8 a resolution (cpd 4)
4A0B · DNA damage-binding protein 1: “Structure of HSDDB1-DRDDB2 bound to a 16 bp cpd-duplex (pyrimidine at D-1 position) at 3.8 a resolution (cpd…”. X-ray diffraction, 20 pockets (best druggability 0.85). MolNFT v1 #85049 on GenesisL1: 3D…
- PDB
- 4A0B
- Type
- protein + DNA
- Length
- 2,948 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA damage-binding protein 1; DNA damage-binding protein 2…
- UniProt
- Q16531, Q2YDS1
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 8 distinct chains · 5% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA damage-binding protein 1 | protein | 1090 | 4% helix, 49% strand | Q16531 |
| B | DNA damage-binding protein 2 | protein | 354 | 7% helix, 43% strand | Q2YDS1 |
| C | DNA damage-binding protein 1 | protein | 1095 | 5% helix, 49% strand | Q16531 |
| D | DNA damage-binding protein 2 | protein | 355 | 7% helix, 42% strand | Q2YDS1 |
| G | 5'-D(*DGP*GP*TP*GP*AP*AP*AP*(TTD)P*AP*GP*CP*AP*GP*DGP)-3' | dna | 14 | — | — |
| H | 5'-D(*CP*CP*TP*GP*CP*TP*CP*CP*TP*TP*TP*CP*AP*CP*CP*C)-3' | dna | 14 | — | — |
| I | 5'-D(*DGP*GP*TP*GP*AP*AP*AP*(TTD)P*AP*GP*CP*AP*GP*DGP)-3' | dna | 13 | — | — |
| J | 5'-D(*CP*CP*TP*GP*CP*TP*CP*CP*TP*TP*TP*CP*AP*CP*CP*C)-3' | dna | 13 | — | — |
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 | 912 | 0.85 | 0.86 | 73 | empty |
| 2 | 1160 | 0.83 | 0.84 | 81 | empty |
| 3 | 1100 | 0.82 | 0.83 | 95 | empty |
| 4 | 1044 | 0.81 | 0.82 | 91 | empty |
| 5 | 446 | 0.80 | 0.88 | 61 | empty |
Interfaces
13 interfaces between chains.
- C–D · 2519 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 2338 Ų buried · 19 hydrogen bonds · protein-protein
- B–G · 680 Ų buried · 13 hydrogen bonds · protein-nucleic
- D–I · 677 Ų buried · 14 hydrogen bonds · protein-nucleic
- G–H · 580 Ų buried · 37 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 4A0B · Structure of hsDDB1-drDDB2 bound to a 16 bp CPD-duplex (pyrimidine at D-1 position) at… · the same entry in another collection · chain I against I, TM-score 1.00
- Q2YDS1 · AlphaFold monomer V2.0 prediction for DNA damage-binding protein 2 (Q2YDS1) · a predicted model of the same protein · chain B against A, TM-score 0.98
- Q16531 · AlphaFold monomer V2.0 prediction for DNA damage-binding protein 1 (Q16531) · a predicted model of the same protein · chain C against A, TM-score 0.86
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 Q2YDS1
- Elsewhere: RCSB PDB 4A0B · PDBe 4A0B · UniProt Q16531 · UniProt Q2YDS1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.