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Substrate-bound crystal structure of 2-dehydro-3-deoxyphosphooctonate aldolase from burkholderia pseudomallei
Analyse Substrate-bound crystal structure of 2-dehydro-3-deoxyphosphooctonate aldolase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3UND
- Type
- protein
- Length
- 1,133 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
- Ligands
- A5P, PEP, KD0
- Pockets
- 13 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-dehydro-3-deoxyphosphooctonate aldolase 2 (EC 2.5.1.55) | protein | 283 | 41% helix, 21% strand | Q3JP68 |
| B, D | 2-dehydro-3-deoxyphosphooctonate aldolase 2 (EC 2.5.1.55) | protein | 284 | 41% helix, 21% strand | Q3JP68 |
| C | 2-dehydro-3-deoxyphosphooctonate aldolase 2 (EC 2.5.1.55) | protein | 282 | 42% helix, 21% strand | Q3JP68 |
Ligands and binding sites
- A5P · Arabinose-5-phosphate · ligand · 4 copies · chains A, C, B, D
- PEP · Phosphoenolpyruvate · ligand · 4 copies · chains A, B, C, D
- KD0 · 3-deoxy-8-O-phosphono-D-manno-oct-2-ulosonic acid · ligand · 4 copies · chains A, C, B, D
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 232 | 0.82 | 0.95 | 45 | A5P, PEP, KD0, EDO |
| 2 | 259 | 0.82 | 0.94 | 53 | A5P, PEP, KD0 |
| 3 | 235 | 0.82 | 0.94 | 47 | A5P, PEP, KD0, EDO |
| 4 | 227 | 0.81 | 0.94 | 45 | A5P, PEP, KD0, EDO |
| 5 | 153 | 0.66 | 0.87 | 26 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2002 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 1960 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 1937 Ų buried · 31 hydrogen bonds · protein-protein
- B–D · 1908 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 209 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3UND · Substrate-bound crystal structure of 2-dehydro-3-deoxyphosphooctonate aldolase from… · 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 3UND · PDBe 3UND · UniProt Q3JP68
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