Research workbench
Crystal structure of glycinamide formyltransferase (purn) from mycobacterium tuberculosis in complex with 5-methyl-5,6,7,8- tetrahydrofolic acid derivative
Analyse Crystal structure of glycinamide formyltransferase (purn) from mycobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DCJ
- Type
- protein
- Length
- 411 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable 5'-phosphoribosylglycinamide formyltransferase purn
- EC
- 2.1.2.2
- UniProt
- P71554
- Ligands
- THH, MG, CL, NO3
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable 5'-phosphoribosylglycinamide formyltransferase purn (EC 2.1.2.2) | protein | 206 | 36% helix, 25% strand | P71554 |
| B | Probable 5'-phosphoribosylglycinamide formyltransferase purn (EC 2.1.2.2) | protein | 205 | 36% helix, 27% strand | P71554 |
Ligands and binding sites
- THH · N-[4-({[(6S)-2-amino-4-hydroxy-5-methyl-5,6,7,8-tetrahydropteridin-6-yl]methyl}amino)benzoyl]-L-glutamic acid · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains A
- CL · Chloride ion · ion · 2 copies · chains A, B
- NO3 · Nitrate ion · ion · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 658 | 0.73 | 0.80 | 55 | THH, MG |
| 2 | 386 | 0.66 | 0.80 | 39 | THH |
| 3 | 125 | 0.49 | 0.79 | 30 | empty |
| 4 | 54 | 0.42 | 0.83 | 18 | NO3 |
Interfaces
1 interface between chains.
- A–B · 703 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 3DCJ · Crystal structure of glycinamide formyltransferase (PurN) from Mycobacterium tuberculosis… · 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 P71554
- Elsewhere: RCSB PDB 3DCJ · PDBe 3DCJ · UniProt P71554
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