Research workbench
Crystal structure of 2-dehydro-3-deoxyphosphooctonate aldolase from burkholderia cenocepacia
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
- 3TML
- Type
- protein
- Length
- 1,054 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-dehydro-3-deoxyphosphooctonate aldolase
- EC
- 2.5.1.55
- UniProt
- B4EDA2
- Ligands
- SO4, CL
- Pockets
- 10 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-dehydro-3-deoxyphosphooctonate aldolase (EC 2.5.1.55) | protein | 262 | 47% helix, 19% strand | B4EDA2 |
| B, C, D | 2-dehydro-3-deoxyphosphooctonate aldolase (EC 2.5.1.55) | protein | 264 | 47% helix, 19% strand | B4EDA2 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains B, D, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 686 | 0.78 | 0.83 | 80 | empty |
| 2 | 497 | 0.70 | 0.80 | 33 | empty |
| 3 | 351 | 0.60 | 0.77 | 34 | empty |
| 4 | 101 | 0.39 | 0.76 | 20 | SO4 |
| 5 | 102 | 0.37 | 0.75 | 24 | SO4 |
Interfaces
5 interfaces between chains.
- A–C · 1740 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 1612 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 468 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 173 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 71 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3TML · Crystal structure of 2-dehydro-3-deoxyphosphooctonate aldolase from Burkholderia… · the same entry in another collection · chain A against A, TM-score 1.00
- B4EDA2 · AlphaFold monomer V2.0 prediction for 2-dehydro-3-deoxyphosphooctonate aldolase (B4EDA2) · a predicted model of the same protein · chain B 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 B4EDA2
- Elsewhere: RCSB PDB 3TML · PDBe 3TML · UniProt B4EDA2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.