Research workbench
L-rhamnulose-1-phosphate aldolase from escherichia COLI (mutant A88F- E192A)
Analyse L-rhamnulose-1-phosphate aldolase from escherichia COLI (mutant A88F- E192A) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2V9N
- Type
- protein
- Length
- 1,096 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rhamnulose-1-phosphate aldolase
- EC
- 4.1.2.19
- UniProt
- P32169
- Ligands
- ZN, PO4
- Pockets
- 14 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Rhamnulose-1-phosphate aldolase (EC 4.1.2.19) | protein | 274 | 45% helix, 17% strand | P32169 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 10 copies · chains A, B, C, D
- PGO · S-1,2-propanediol · additive · 8 copies · chains A, C, B, D
- GOL · Glycerol · additive · 5 copies · chains A, B, D, C
- CIT · Citric acid · additive · 4 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1063 | 0.82 | 0.83 | 67 | empty |
| 2 | 153 | 0.63 | 0.85 | 28 | CIT, PO4 |
| 3 | 161 | 0.62 | 0.85 | 28 | CIT, PO4 |
| 4 | 139 | 0.61 | 0.85 | 25 | CIT, PO4 |
| 5 | 166 | 0.61 | 0.83 | 28 | ZN, CIT, PO4 |
Interfaces
4 interfaces between chains.
- A–C · 1414 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 1412 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 1411 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 1395 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 2V9N · L-rhamnulose-1-phosphate aldolase from escherichia COLI (mutant A88F- E192A) · the same entry in another collection · chain A against A, TM-score 1.00
- P32169 · AlphaFold monomer V2.0 prediction for rhamnulose-1-phosphate aldolase (P32169) · a predicted model of the same protein · 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 P32169
- Elsewhere: RCSB PDB 2V9N · PDBe 2V9N · UniProt P32169
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