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Crystal structure of deoxyribose phosphate aldolase from mycobacterium avium 104 in a schiff base with an unknown aldehyde
Analyse Crystal structure of deoxyribose phosphate aldolase from mycobacterium avium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NG3
- Type
- protein
- Length
- 873 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxyribose-phosphate aldolase
- EC
- 4.1.2.4
- UniProt
- A0QLL2
- Ligands
- UNL, CL
- Pockets
- 7 · best druggability 0.65
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deoxyribose-phosphate aldolase (EC 4.1.2.4) | protein | 219 | 49% helix, 16% strand | A0QLL2 |
| B | Deoxyribose-phosphate aldolase (EC 4.1.2.4) | protein | 216 | 50% helix, 16% strand | A0QLL2 |
| C | Deoxyribose-phosphate aldolase (EC 4.1.2.4) | protein | 220 | 49% helix, 16% strand | A0QLL2 |
| D | Deoxyribose-phosphate aldolase (EC 4.1.2.4) | protein | 218 | 49% helix, 16% strand | A0QLL2 |
Ligands and binding sites
- UNL · Unknown ligand · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 226 | 0.65 | 0.83 | 45 | UNL |
| 2 | 254 | 0.64 | 0.82 | 44 | UNL |
| 3 | 540 | 0.63 | 0.75 | 72 | EDO |
| 4 | 479 | 0.61 | 0.75 | 76 | EDO |
| 5 | 140 | 0.52 | 0.80 | 24 | UNL |
Interfaces
6 interfaces between chains.
- C–D · 1210 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1201 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 360 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 340 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 59 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 3NG3 · Crystal structure of deoxyribose phosphate aldolase from mycobacterium avium 104 in a… · the same entry in another collection · chain D against D, TM-score 1.00
- A0QLL2 · AlphaFold monomer V2.0 prediction for deoxyribose-phosphate aldolase (A0QLL2) · a predicted model of the same protein · chain D 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 A0QLL2
- Elsewhere: RCSB PDB 3NG3 · PDBe 3NG3 · UniProt A0QLL2
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