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Crystal structure of phospho-2-dehydro-3-deoxyheptonate aldolase (dahp synthase) (TM0343) from thermotoga maritima at 1.92 a resolution
Analyse Crystal structure of phospho-2-dehydro-3-deoxyheptonate aldolase (dahp… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1VR6
- Type
- protein
- Length
- 1,360 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phospho-2-dehydro-3-deoxyheptonate aldolase
- EC
- 2.5.1.54
- UniProt
- Q9WYH8
- Pockets
- 19 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phospho-2-dehydro-3-deoxyheptonate aldolase (EC 2.5.1.54) | protein | 343 | 38% helix, 24% strand | Q9WYH8 |
| B | Phospho-2-dehydro-3-deoxyheptonate aldolase (EC 2.5.1.54) | protein | 338 | 36% helix, 24% strand | Q9WYH8 |
| C | Phospho-2-dehydro-3-deoxyheptonate aldolase (EC 2.5.1.54) | protein | 339 | 38% helix, 23% strand | Q9WYH8 |
| D | Phospho-2-dehydro-3-deoxyheptonate aldolase (EC 2.5.1.54) | protein | 340 | 36% helix, 22% strand | Q9WYH8 |
Pockets
19 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 799 | 0.81 | 0.84 | 90 | empty |
| 2 | 942 | 0.80 | 0.82 | 76 | empty |
| 3 | 782 | 0.78 | 0.82 | 69 | empty |
| 4 | 61 | 0.74 | 0.99 | 17 | empty |
| 5 | 465 | 0.69 | 0.80 | 54 | empty |
Interfaces
6 interfaces between chains.
- A–C · 1841 Ų buried · 39 hydrogen bonds · protein-protein
- A–B · 1391 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 1367 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 1084 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 1062 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 1VR6 · Crystal structure of Phospho-2-dehydro-3-deoxyheptonate aldolase (DAHP synthase) (TM0343)… · the same entry in another collection · chain D against D, TM-score 1.00
- Q9WYH8 · AlphaFold monomer V2.0 prediction for phospho-2-dehydro-3-deoxyheptonate aldolase (Q9WYH8) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 Q9WYH8
- Elsewhere: RCSB PDB 1VR6 · PDBe 1VR6 · UniProt Q9WYH8
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