Research workbench
3-deoxy-D-arabino-heptulosonate 7-phosphate synthase with D-tryptophan bound in the tryptophan and phenylalanine binding sites
Analyse 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase with D-tryptophan bound in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5E5G
- Type
- protein
- Length
- 914 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase
- EC
- 2.5.1.54
- UniProt
- A0A0E8NFD1
- Ligands
- DTR, MN, SO4
- Pockets
- 9 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase (EC 2.5.1.54) | protein | 458 | 42% helix, 14% strand | A0A0E8NFD1 |
| B | 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase (EC 2.5.1.54) | protein | 456 | 43% helix, 15% strand | A0A0E8NFD1 |
Ligands and binding sites
- DTR · D-tryptophan · ligand · 4 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 828 | 0.75 | 0.79 | 82 | DTR |
| 2 | 227 | 0.68 | 0.85 | 36 | DTR |
| 3 | 253 | 0.68 | 0.84 | 35 | DTR |
| 4 | 471 | 0.62 | 0.76 | 65 | SO4 |
| 5 | 303 | 0.61 | 0.79 | 37 | SO4 |
Interfaces
1 interface between chains.
- A–B · 1689 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 5E5G · 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase with D-tryptophan bound in the… · 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 A0A0E8NFD1
- Elsewhere: RCSB PDB 5E5G · PDBe 5E5G · UniProt A0A0E8NFD1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.