Research workbench
Crystal structure of formyltetrahydrofolate deformylase (YP_105254.1) from burkholderia mallei atcc 23344 at 1.90 a resolution
Analyse Crystal structure of formyltetrahydrofolate deformylase (YP_105254.1) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LOU
- Type
- protein
- Length
- 1,120 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Formyltetrahydrofolate deformylase
- EC
- 3.5.1.10
- UniProt
- Q62DH4
- Ligands
- UNL, SO4
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Formyltetrahydrofolate deformylase (EC 3.5.1.10) | protein | 281 | 35% helix, 31% strand | Q62DH4 |
| B, D | Formyltetrahydrofolate deformylase (EC 3.5.1.10) | protein | 279 | 36% helix, 31% strand | Q62DH4 |
Ligands and binding sites
- UNL · Unknown ligand · ligand · chains A
- SO4 · Sulfate ion · ion · 12 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 23 copies · chains A, C, B, D
- PEG · Di(hydroxyethyl)ether · additive · 7 copies · chains B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 906 | 0.82 | 0.84 | 105 | EDO |
| 2 | 819 | 0.80 | 0.83 | 82 | EDO, PEG |
| 3 | 350 | 0.67 | 0.81 | 36 | EDO |
| 4 | 224 | 0.60 | 0.81 | 36 | empty |
| 5 | 218 | 0.59 | 0.81 | 34 | UNL |
Interfaces
6 interfaces between chains.
- A–B · 1576 Ų buried · 33 hydrogen bonds · protein-protein
- C–D · 1559 Ų buried · 32 hydrogen bonds · protein-protein
- A–D · 531 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 510 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 355 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 3LOU · Crystal structure of Formyltetrahydrofolate deformylase (YP_105254.1) from BURKHOLDERIA… · the same entry in another collection · chain C against C, 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 Q62DH4
- Elsewhere: RCSB PDB 3LOU · PDBe 3LOU · UniProt Q62DH4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.