MolNFT v1 · #112027 · protein
Crystal structure of DCAF1/SIV-mnd VPX/MND SAMHD1 ntd ternary complex
4Z8L · Protein vprbp: “Crystal structure of DCAF1/SIV-mnd VPX/MND SAMHD1 ntd ternary complex”. X-ray diffraction, 1 ligand (ZN), 13 pockets (best druggability 0.83). MolNFT v1 #112027 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 4Z8L
- Type
- protein
- Length
- 955 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein vprbp; Vpx protein; SAM domain and hd domain-containing protein
- EC
- 2.7.11.1
- UniProt
- Q9Y4B6, Q7ZB17, H6WEA4
- Ligands
- ZN
- Pockets
- 13 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 20% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Protein vprbp (EC 2.7.11.1) | protein | 305 | 2% helix, 50% strand | Q9Y4B6 |
| B, E | Vpx protein | protein | 79 | 65% helix, 1% strand | Q7ZB17 |
| C | SAM domain and hd domain-containing protein | protein | 92 | 24% helix, 1% strand | H6WEA4 |
| F | SAM domain and hd domain-containing protein | protein | 95 | 35% helix, 1% strand | H6WEA4 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1124 | 0.83 | 0.83 | 81 | empty |
| 2 | 1128 | 0.82 | 0.83 | 76 | empty |
| 3 | 91 | 0.67 | 0.91 | 18 | empty |
| 4 | 382 | 0.66 | 0.80 | 45 | empty |
| 5 | 260 | 0.57 | 0.78 | 29 | empty |
Interfaces
8 interfaces between chains.
- D–E · 1557 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 1550 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 1532 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1501 Ų buried · 14 hydrogen bonds · protein-protein
- D–F · 607 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 4Z8L · Crystal structure of DCAF1/SIV-MND VPX/MND SAMHD1 NTD ternary complex · the same entry in another collection · chain F against F, 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 D against A, TM-score 0.98
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 Q9Y4B6
- Every structure of UniProt Q7ZB17
- Every structure of UniProt H6WEA4
- Elsewhere: RCSB PDB 4Z8L · PDBe 4Z8L · UniProt Q9Y4B6 · UniProt Q7ZB17 · UniProt H6WEA4
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