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Crystal structure wlard, a sugar 3N-formyl transferase in the presence of dtdp and 10-N-formyl-thf
Analyse Crystal structure wlard, a sugar 3N-formyl transferase in the presence of dtdp… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LXY
- Type
- protein
- Length
- 544 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Wlard, a sugar 3N-formyl transferase
- UniProt
- A8FMJ3
- Ligands
- 1YA, TYD
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Wlard, a sugar 3N-formyl transferase | protein | 272 | 26% helix, 27% strand | A8FMJ3 |
| B | Wlard, a sugar 3N-formyl transferase | protein | 272 | 25% helix, 27% strand | A8FMJ3 |
Ligands and binding sites
- 1YA · N-{4-[{[(6S)-2-amino-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}(formyl)amino]benzoyl}-L-glutamic acid · ligand · 2 copies · chains A, B
- TYD · Thymidine-5'-diphosphate · ligand · 2 copies · chains A, B
- MPO · 3[N-morpholino]propane sulfonic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 421 | 0.73 | 0.83 | 44 | 1YA, TYD |
| 2 | 438 | 0.72 | 0.82 | 42 | 1YA, TYD |
| 3 | 683 | 0.71 | 0.78 | 44 | empty |
| 4 | 87 | 0.46 | 0.81 | 14 | empty |
| 5 | 90 | 0.43 | 0.79 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1316 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 4LXY · Crystal structure WlaRD, a sugar 3N-formyl transferase in the presence of dTDP and… · 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 A8FMJ3
- Elsewhere: RCSB PDB 4LXY · PDBe 4LXY · UniProt A8FMJ3
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