Research workbench
Crystal structure of 2-dehydro-3-deoxyphosphogluconate ALDOLASE/4- hydroxy-2-oxoglutarate aldolase (TM0066) from thermotoga maritima at 2.30 a resolution
Analyse Crystal structure of 2-dehydro-3-deoxyphosphogluconate ALDOLASE/4… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1VLW
- Type
- protein
- Length
- 616 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-dehydro-3-deoxyphosphogluconate ALDOLASE/4-hydroxy-2- oxoglutarate aldolase
- EC
- 4.1.2.14, 4.1.3.16
- UniProt
- Q9WXS1
- Pockets
- 6 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-dehydro-3-deoxyphosphogluconate ALDOLASE/4-hydroxy-2- oxoglutarate aldolase (EC 4.1.2.14, 4.1.3.16) | protein | 205 | 47% helix, 16% strand | Q9WXS1 |
| B | 2-dehydro-3-deoxyphosphogluconate ALDOLASE/4-hydroxy-2- oxoglutarate aldolase (EC 4.1.2.14, 4.1.3.16) | protein | 207 | 48% helix, 17% strand | Q9WXS1 |
| C | 2-dehydro-3-deoxyphosphogluconate ALDOLASE/4-hydroxy-2- oxoglutarate aldolase (EC 4.1.2.14, 4.1.3.16) | protein | 204 | 48% helix, 17% strand | Q9WXS1 |
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 363 | 0.56 | 0.75 | 50 | empty |
| 2 | 157 | 0.49 | 0.78 | 23 | empty |
| 3 | 87 | 0.40 | 0.78 | 15 | empty |
| 4 | 90 | 0.36 | 0.75 | 23 | empty |
| 5 | 51 | 0.32 | 0.77 | 14 | empty |
Interfaces
2 interfaces between chains.
- B–C · 633 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 230 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 1VLW · Crystal structure of 2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate… · 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 Q9WXS1
- Elsewhere: RCSB PDB 1VLW · PDBe 1VLW · UniProt Q9WXS1
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