MolNFT v1 · #172266 · protein
Crystal structure of SIV VPR,FUSED to T4 lysozyme, isolated from moustached monkey, bound to human DDB1 and human DCAF1 (amino acid residues 1046-1396)
6ZX9 · DNA damage-binding protein 1: “Crystal structure of SIV VPR,FUSED to T4 lysozyme, isolated from moustached monkey, bound to human DDB1 and…”. X-ray diffraction, 1 ligand (ZN), 20 pockets (best druggability 0.85). MolNFT v1 #172266…
- PDB
- 6ZX9
- Type
- protein
- Length
- 1,716 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA damage-binding protein 1; DDB1- and CUL4-associated factor 1; Vpr protein fused to T4…
- EC
- 2.7.11.1, 3.2.1.17
- UniProt
- Q16531, Q9Y4B6, P00720, A4UDG5
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 14% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA damage-binding protein 1 | protein | 1124 | 6% helix, 52% strand | Q16531 |
| B | DDB1- and CUL4-associated factor 1 (EC 2.7.11.1) | protein | 335 | 7% helix, 45% strand | Q9Y4B6 |
| C | Vpr protein fused to T4 lysozyme (EC 3.2.1.17) | protein | 257 | 60% helix, 6% strand | P00720, A4UDG5 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 797 | 0.85 | 0.88 | 74 | GOL |
| 2 | 846 | 0.81 | 0.84 | 81 | GOL |
| 3 | 913 | 0.76 | 0.79 | 64 | empty |
| 4 | 550 | 0.76 | 0.83 | 45 | empty |
| 5 | 713 | 0.75 | 0.81 | 73 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2319 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 1763 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 279 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6ZX9 · Crystal structure of SIV Vpr,fused to T4 lysozyme, isolated from moustached monkey, bound… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9Y4B6 · AlphaFold monomer V2.0 prediction for DDB1- and CUL4-associated factor 1 (Q9Y4B6) · 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 0.87
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 Q9Y4B6
- Every structure of UniProt P00720
- Every structure of UniProt A4UDG5
- Elsewhere: RCSB PDB 6ZX9 · PDBe 6ZX9 · UniProt Q16531 · UniProt Q9Y4B6 · UniProt P00720 · UniProt A4UDG5
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