MolNFT v1 · #51509 · protein
L-rhamnulose-1-phosphate aldolase from escherichia COLI (mutant A87M- T109F-E192A)
2V9M: “L-rhamnulose-1-phosphate aldolase from escherichia COLI (mutant A87M- T109F-E192A)”. X-ray diffraction, 2 ligands (ZN, CA), 4 pockets (best druggability 0.49). MolNFT v1 #51509 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 2V9M
- Type
- protein
- Length
- 548 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, CA
- Pockets
- 4 · best druggability 0.49
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Rhamnulose-1-phosphate aldolase (EC 4.1.2.19) | protein | 274 | 47% helix, 16% strand | P32169 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B
- CA · Calcium ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, B
- CIT · Citric acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 119 | 0.49 | 0.80 | 29 | ZN |
| 2 | 70 | 0.30 | 0.74 | 16 | empty |
| 3 | 52 | 0.30 | 0.76 | 17 | empty |
| 4 | 62 | 0.29 | 0.74 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 11 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2V9M · L-rhamnulose-1-phosphate aldolase from escherichia COLI (mutant A87M- T109F-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 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 2V9M · PDBe 2V9M · UniProt P32169
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