MolNFT v1 · #51505 · protein
L-rhamnulose-1-phosphate aldolase from escherichia COLI ( mutant E192A-K248W-L274STOP)
2V9I: “L-rhamnulose-1-phosphate aldolase from escherichia COLI ( mutant E192A-K248W-L274STOP)”. X-ray diffraction, 1 ligand (ZN), 4 pockets (best druggability 0.62). MolNFT v1 #51505 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 2V9I
- Type
- protein
- Length
- 544 residues
- Chains
- 2
- 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
- Pockets
- 4 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Rhamnulose-1-phosphate aldolase (EC 4.1.2.19) | protein | 272 | 45% helix, 17% strand | P32169 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 258 | 0.62 | 0.81 | 39 | empty |
| 2 | 61 | 0.29 | 0.74 | 16 | empty |
| 3 | 62 | 0.28 | 0.73 | 14 | empty |
| 4 | 52 | 0.28 | 0.74 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 507 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 2V9I · L-RHAMNULOSE-1-PHOSPHATE ALDOLASE FROM ESCHERICHIA COLI (MUTANT E192A- K248W-L274stop) · 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 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 P32169
- Elsewhere: RCSB PDB 2V9I · PDBe 2V9I · UniProt P32169
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