MolNFT v1 · #85058 · protein + DNA
Structure of DDB1-DDB2-CUL4A-RBX1 bound to a 12 bp abasic site containing DNA-duplex
4A0K · Cullin-4A: “Structure of DDB1-DDB2-CUL4A-RBX1 bound to a 12 bp abasic site containing DNA-duplex”. X-ray diffraction, 20 pockets (best druggability 0.84). MolNFT v1 #85058 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4A0K
- Type
- protein + DNA
- Length
- 2,224 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cullin-4A; E3 ubiquitin-protein ligase RBX1; DNA damage-binding protein 1; DNA…
- EC
- 6.3.2.-
- UniProt
- Q13619, P62878, Q16531, Q2YDS1
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 6 distinct chains · 23% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cullin-4A | protein | 719 | 60% helix, 5% strand | Q13619 |
| B | E3 ubiquitin-protein ligase RBX1 (EC 6.3.2.-) | protein | 21 | 0% helix, 67% strand | P62878 |
| C | DNA damage-binding protein 1 | protein | 1105 | 6% helix, 49% strand | Q16531 |
| D | DNA damage-binding protein 2 | protein | 355 | 6% helix, 45% strand | Q2YDS1 |
| E | 12 bp thf containing DNA | dna | 12 | — | — |
| F | 12 bp DNA | dna | 12 | — | — |
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1163 | 0.84 | 0.85 | 102 | empty |
| 2 | 1150 | 0.82 | 0.83 | 100 | empty |
| 3 | 509 | 0.80 | 0.87 | 71 | empty |
| 4 | 1045 | 0.79 | 0.81 | 122 | empty |
| 5 | 599 | 0.78 | 0.84 | 49 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1690 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 1582 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 1561 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 597 Ų buried · 6 hydrogen bonds · protein-nucleic
- E–F · 477 Ų buried · 49 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 4A0K · Structure of DDB1-DDB2-CUL4A-RBX1 bound to a 12 bp abasic site containing DNA-duplex · the same entry in another collection · chain F against F, TM-score 1.00
- Q13619 · AlphaFold monomer V2.0 prediction for cullin-4A (Q13619) · a predicted model of the same protein · chain A against A, TM-score 0.98
- Q2YDS1 · AlphaFold monomer V2.0 prediction for DNA damage-binding protein 2 (Q2YDS1) · a predicted model of the same protein · chain D 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 C against A, TM-score 0.83
- P62878 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase RBX1 (P62878) · a predicted model of the same protein · chain B against A, TM-score 0.26
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 Q13619
- Every structure of UniProt P62878
- Every structure of UniProt Q16531
- Every structure of UniProt Q2YDS1
- Elsewhere: RCSB PDB 4A0K · PDBe 4A0K · UniProt Q13619 · UniProt P62878 · UniProt Q16531 · UniProt Q2YDS1
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