Research workbench
Unexpected formation of an epoxide-derived multisubstrate adduct inhibitor on the active site of gar transformylase
Analyse Unexpected formation of an epoxide-derived multisubstrate adduct inhibitor on… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1JKX
- Type
- protein
- Length
- 836 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoribosylglycinamide formyltransferase
- EC
- 2.1.2.2
- UniProt
- P08179
- Ligands
- 138
- Pockets
- 7 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Phosphoribosylglycinamide formyltransferase (EC 2.1.2.2) | protein | 209 | 35% helix, 25% strand | P08179 |
Ligands and binding sites
- 138 · N-[5'-O-phosphono-ribofuranosyl]-2-[2-hydroxy-2-[4-[glutamic acid]-N-carbonylphenyl]-3-[2-amino-4-hydroxy-quinazolin-6-yl]-propanylamino]-acetamide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 440 | 0.63 | 0.77 | 39 | 138 |
| 2 | 413 | 0.62 | 0.77 | 41 | 138 |
| 3 | 376 | 0.61 | 0.77 | 41 | 138 |
| 4 | 360 | 0.59 | 0.76 | 42 | 138 |
| 5 | 317 | 0.58 | 0.76 | 29 | empty |
Interfaces
3 interfaces between chains.
- A–B · 532 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 26 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 20 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1JKX · Unexpected formation of an epoxide-derived multisubstrate adduct inhibitor on the active… · the same entry in another collection · chain D against D, TM-score 1.00
- P08179 · AlphaFold monomer V2.0 prediction for phosphoribosylglycinamide formyltransferase (P08179) · a predicted model of the same protein · chain B 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 P08179
- Elsewhere: RCSB PDB 1JKX · PDBe 1JKX · UniProt P08179
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