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Crystal structure of 2-dehydro-3-deoxyphosphooctonate aldolase from burkholderia pseudomallei
Analyse Crystal structure of 2-dehydro-3-deoxyphosphooctonate aldolase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SZ8
- Type
- protein
- Length
- 1,052 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-dehydro-3-deoxyphosphooctonate aldolase 2
- EC
- 2.5.1.55
- UniProt
- Q3JP68
- Pockets
- 11 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-dehydro-3-deoxyphosphooctonate aldolase 2 (EC 2.5.1.55) | protein | 264 | 40% helix, 22% strand | Q3JP68 |
| B | 2-dehydro-3-deoxyphosphooctonate aldolase 2 (EC 2.5.1.55) | protein | 262 | 39% helix, 21% strand | Q3JP68 |
| C | 2-dehydro-3-deoxyphosphooctonate aldolase 2 (EC 2.5.1.55) | protein | 264 | 40% helix, 21% strand | Q3JP68 |
| D | 2-dehydro-3-deoxyphosphooctonate aldolase 2 (EC 2.5.1.55) | protein | 262 | 39% helix, 21% strand | Q3JP68 |
Ligands and binding sites
- ACT · Acetate ion · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 804 | 0.81 | 0.84 | 70 | empty |
| 2 | 697 | 0.78 | 0.83 | 65 | empty |
| 3 | 589 | 0.74 | 0.81 | 63 | empty |
| 4 | 471 | 0.70 | 0.80 | 52 | empty |
| 5 | 181 | 0.66 | 0.85 | 25 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1607 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 1602 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 1580 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 1499 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 204 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3SZ8 · Crystal structure of 2-dehydro-3-deoxyphosphooctonate aldolase from Burkholderia… · 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 Q3JP68
- Elsewhere: RCSB PDB 3SZ8 · PDBe 3SZ8 · UniProt Q3JP68
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