MolNFT v1 · #17011 · protein
Crystal structure of the tyrosine-regulated 3-deoxy-D-arabino- heptulosonate-7-phosphate synthase from saccharomyces cerevisiae complexed with phenylalanine and manganese
1OFR · Phospho-2-dehydro-3-deoxyheptonate aldolase: “Crystal structure of the tyrosine-regulated 3-deoxy-D-arabino- heptulosonate-7-phosphate synthase from…”. X-ray diffraction, 2 ligands (PHE, MN), 20 pockets (best druggability 0.75).…
- PDB
- 1OFR
- Type
- protein
- Length
- 2,767 residues
- Chains
- 8
- 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
- Ligands
- PHE, MN
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 8 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phospho-2-dehydro-3-deoxyheptonate aldolase (EC 4.1.2.15) | protein | 349 | 39% helix, 17% strand | P32449 |
| B | Phospho-2-dehydro-3-deoxyheptonate aldolase (EC 4.1.2.15) | protein | 347 | 40% helix, 17% strand | P32449 |
| C | Phospho-2-dehydro-3-deoxyheptonate aldolase (EC 4.1.2.15) | protein | 348 | 40% helix, 18% strand | P32449 |
| D | Phospho-2-dehydro-3-deoxyheptonate aldolase (EC 4.1.2.15) | protein | 350 | 40% helix, 17% strand | P32449 |
| E | Phospho-2-dehydro-3-deoxyheptonate aldolase (EC 4.1.2.15) | protein | 338 | 39% helix, 19% strand | P32449 |
| F | Phospho-2-dehydro-3-deoxyheptonate aldolase (EC 4.1.2.15) | protein | 346 | 38% helix, 20% strand | P32449 |
| G | Phospho-2-dehydro-3-deoxyheptonate aldolase (EC 4.1.2.15) | protein | 343 | 38% helix, 20% strand | P32449 |
| H | Phospho-2-dehydro-3-deoxyheptonate aldolase (EC 4.1.2.15) | protein | 346 | 38% helix, 18% strand | P32449 |
Ligands and binding sites
- PHE · Phenylalanine · ligand · 4 copies · chains C, D, G, H
- MN · Manganese (II) ion · metal · 8 copies · chains A, H, C, D, E, F, G, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 446 | 0.75 | 0.84 | 58 | MN |
| 2 | 532 | 0.75 | 0.83 | 69 | MN |
| 3 | 101 | 0.75 | 0.96 | 22 | empty |
| 4 | 809 | 0.75 | 0.79 | 83 | empty |
| 5 | 432 | 0.75 | 0.84 | 65 | empty |
Interfaces
15 interfaces between chains.
- A–B · 3112 Ų buried · 50 hydrogen bonds · protein-protein
- G–H · 3077 Ų buried · 50 hydrogen bonds · protein-protein
- C–D · 3046 Ų buried · 50 hydrogen bonds · protein-protein
- E–F · 2958 Ų buried · 47 hydrogen bonds · protein-protein
- B–F · 381 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 1OFR · Crystal structure of the tyrosine-regulated 3-deoxy-D-arabino-heptulosonate-7-phosphate… · the same entry in another collection · chain H against H, 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 F against A, TM-score 0.99
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 1OFR · PDBe 1OFR · UniProt P32449
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