MolNFT v1 · #51628 · protein
The structure of histidine inhibited hisg from methanobacterium thermoautotrophicum
2VD3 · ATP phosphoribosyltransferase: “The structure of histidine inhibited hisg from methanobacterium thermoautotrophicum”. X-ray diffraction, 3 ligands (HIS, MG, CL), 5 pockets (best druggability 0.67). MolNFT v1 #51628 on GenesisL1: 3D…
- PDB
- 2VD3
- Type
- protein
- Length
- 577 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP phosphoribosyltransferase
- EC
- 2.4.2.17
- UniProt
- O27550
- Ligands
- HIS, MG, CL
- Pockets
- 5 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP phosphoribosyltransferase (EC 2.4.2.17) | protein | 289 | 30% helix, 33% strand | O27550 |
| B | ATP phosphoribosyltransferase (EC 2.4.2.17) | protein | 288 | 33% helix, 33% strand | O27550 |
Ligands and binding sites
- HIS · Histidine · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 9 copies · chains A, B
- CL · Chloride ion · ion · 9 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 5 copies · chains A, B
- IMD · Imidazole · additive · 3 copies · chains A, B
- MRD · (4R)-2-methylpentane-2,4-diol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 739 | 0.67 | 0.75 | 66 | CL, MG, MPD |
| 2 | 94 | 0.49 | 0.81 | 16 | empty |
| 3 | 87 | 0.46 | 0.81 | 16 | MG |
| 4 | 99 | 0.36 | 0.74 | 16 | empty |
| 5 | 92 | 0.36 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 843 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 2VD3 · The structure of histidine inhibited HisG from Methanobacterium thermoautotrophicum · the same entry in another collection · chain A against A, TM-score 1.00
- O27550 · AlphaFold monomer V2.0 prediction for ATP phosphoribosyltransferase (O27550) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 O27550
- Elsewhere: RCSB PDB 2VD3 · PDBe 2VD3 · UniProt O27550
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.