Research workbench
Crystal structure of the tyrosine-regulated 3-deoxy-D-arabino- heptulosonate-7-phosphate synthase from saccharomyces cerevisiae
Analyse Crystal structure of the tyrosine-regulated 3-deoxy-D-arabino… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1OFP
- Type
- protein
- Length
- 1,259 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phospho-2-dehydro-3-deoxyheptonate aldolase
- EC
- 4.1.2.15
- UniProt
- P32449
- Pockets
- 13 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phospho-2-dehydro-3-deoxyheptonate aldolase (EC 4.1.2.15) | protein | 306 | 42% helix, 20% strand | P32449 |
| B | Phospho-2-dehydro-3-deoxyheptonate aldolase (EC 4.1.2.15) | protein | 321 | 40% helix, 21% strand | P32449 |
| C | Phospho-2-dehydro-3-deoxyheptonate aldolase (EC 4.1.2.15) | protein | 318 | 40% helix, 20% strand | P32449 |
| D | Phospho-2-dehydro-3-deoxyheptonate aldolase (EC 4.1.2.15) | protein | 314 | 41% helix, 21% strand | P32449 |
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1095 | 0.83 | 0.84 | 126 | empty |
| 2 | 906 | 0.82 | 0.84 | 112 | empty |
| 3 | 110 | 0.77 | 0.96 | 28 | empty |
| 4 | 99 | 0.75 | 0.96 | 27 | empty |
| 5 | 177 | 0.57 | 0.81 | 24 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2430 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 2422 Ų buried · 33 hydrogen bonds · protein-protein
- A–D · 336 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 327 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 139 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1OFP · Crystal structure of the tyrosine-regulated 3-deoxy-D-arabino-heptulosonate-7-phosphate… · the same entry in another collection · chain D against D, TM-score 1.00
- P32449 · AlphaFold monomer V2.0 prediction for phospho-2-dehydro-3-deoxyheptonate aldolase… · a predicted model of the same protein · chain B 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 P32449
- Elsewhere: RCSB PDB 1OFP · PDBe 1OFP · UniProt P32449
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.