Research workbench
L-rhamnulose-1-phosphate aldolase from escherichia COLI (mutant Q6Y- L84W-E192A)
Analyse L-rhamnulose-1-phosphate aldolase from escherichia COLI (mutant Q6Y- L84W-E192A) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2V9G
- Type
- protein
- Length
- 1,095 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
- Pockets
- 13 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Rhamnulose-1-phosphate aldolase (EC 4.1.2.19) | protein | 273 | 44% helix, 17% strand | P32169 |
| B, C, D | Rhamnulose-1-phosphate aldolase (EC 4.1.2.19) | protein | 274 | 44% helix, 17% strand | P32169 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- TLA · L(+)-tartaric acid · additive · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1096 | 0.81 | 0.82 | 66 | empty |
| 2 | 145 | 0.62 | 0.85 | 27 | TLA, ZN |
| 3 | 296 | 0.62 | 0.79 | 44 | TLA, ZN |
| 4 | 167 | 0.58 | 0.82 | 25 | TLA, ZN |
| 5 | 137 | 0.56 | 0.83 | 28 | TLA |
Interfaces
4 interfaces between chains.
- B–C · 1502 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 1481 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1429 Ų buried · 26 hydrogen bonds · protein-protein
- A–D · 1414 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 2V9G · L-rhamnulose-1-phosphate aldolase from escherichia COLI (mutant Q6Y- L84W-E192A) · the same entry in another collection · chain B against B, 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 2V9G · PDBe 2V9G · UniProt P32169
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