MolNFT v1 · #137140 · protein
Thermus aquaticus variable protein (taqvp) from diversity-generating retroelements (dgr)
5VF4 · Uncharacterized protein: “Thermus aquaticus variable protein (taqvp) from diversity-generating retroelements (dgr)”. X-ray diffraction, 1 ligand (CA), 10 pockets (best druggability 0.70). MolNFT v1 #137140 on GenesisL1: 3D…
- PDB
- 5VF4
- Type
- protein
- Length
- 1,520 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein
- UniProt
- B7A5T1
- Ligands
- CA
- Pockets
- 10 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Uncharacterized protein | protein | 381 | 16% helix, 24% strand | B7A5T1 |
| C | Uncharacterized protein | protein | 380 | 17% helix, 25% strand | B7A5T1 |
| D | Uncharacterized protein | protein | 378 | 16% helix, 24% strand | B7A5T1 |
Ligands and binding sites
- CA · Calcium ion · metal · 8 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 30 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 745 | 0.70 | 0.77 | 68 | ACT |
| 2 | 687 | 0.69 | 0.77 | 55 | ACT |
| 3 | 781 | 0.69 | 0.76 | 64 | empty |
| 4 | 735 | 0.68 | 0.76 | 81 | ACT |
| 5 | 51 | 0.37 | 0.80 | 22 | empty |
Interfaces
5 interfaces between chains.
- B–C · 630 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 600 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 455 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 331 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 84 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 modified (engineered).
Compared structures
- 5VF4 · Thermus aquaticus variable protein (TaqVP) from diversity-generating retroelements (DGR) · the same entry in another collection · chain A against A, TM-score 1.00
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 B7A5T1
- Elsewhere: RCSB PDB 5VF4 · PDBe 5VF4 · UniProt B7A5T1
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