MolNFT v1 · #24991 · protein
Crystal structure of a phosphoribosyltransferase-related protein from thermus thermophilus
1VCH: “Crystal structure of a phosphoribosyltransferase-related protein from thermus thermophilus”. X-ray diffraction, 2 ligands (CA, CL), 6 pockets (best druggability 0.80). MolNFT v1 #24991 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1VCH
- Type
- protein
- Length
- 832 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoribosyltransferase-related protein
- EC
- 2.4.2.7
- UniProt
- Q5SHW7
- Ligands
- CA, CL
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 5 distinct chains · 24% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoribosyltransferase-related protein (EC 2.4.2.7) | protein | 168 | 27% helix, 36% strand | Q5SHW7 |
| B | Phosphoribosyltransferase-related protein (EC 2.4.2.7) | protein | 170 | 25% helix, 38% strand | Q5SHW7 |
| C | Phosphoribosyltransferase-related protein (EC 2.4.2.7) | protein | 169 | 25% helix, 38% strand | Q5SHW7 |
| D | Phosphoribosyltransferase-related protein (EC 2.4.2.7) | protein | 173 | 25% helix, 38% strand | Q5SHW7 |
| E | Phosphoribosyltransferase-related protein (EC 2.4.2.7) | protein | 152 | 18% helix, 37% strand | Q5SHW7 |
Ligands and binding sites
- CA · Calcium ion · metal · chains C
- CL · Chloride ion · ion · 5 copies · chains A, B, C, D, E
- ACY · Acetic acid · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1161 | 0.80 | 0.81 | 96 | CL, ACY |
| 2 | 916 | 0.79 | 0.81 | 75 | ACY, CL |
| 3 | 822 | 0.78 | 0.81 | 76 | CL, ACY |
| 4 | 264 | 0.61 | 0.80 | 42 | empty |
| 5 | 254 | 0.53 | 0.76 | 29 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1590 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1366 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 373 Ų buried · 3 hydrogen bonds · protein-protein
- B–E · 272 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 269 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 1VCH · Crystal Structure of a Phosphoribosyltransferase-related protein from Thermus thermophilus · 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 Q5SHW7
- Elsewhere: RCSB PDB 1VCH · PDBe 1VCH · UniProt Q5SHW7
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