MolNFT v2 · #160259 · protein
X-ray crystal structure of the YdjI aldolase from Escherichia coli K12
6OFU: “X-ray crystal structure of the YdjI aldolase from Escherichia coli K12”. X-ray diffraction at 1.75, 2 ligands (ZN, CL), 12 pockets (best druggability 0.70). MolNFT v2 #160259 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6OFU
- Type
- protein
- Length
- 1,041 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.75
- Source
- Escherichia coli (strain K12)
- Molecule
- YdjI aldolase
- UniProt
- P77704
- Ligands
- ZN, CL
- Pockets
- 12 · best druggability 0.70
Structure
x-ray diffraction · resolution 1.75 · 4 distinct chains · 52% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | YdjI aldolase | protein | 259 | 52% helix, 17% strand | P77704 |
| B | YdjI aldolase | protein | 264 | 51% helix, 15% strand | P77704 |
| C | YdjI aldolase | protein | 262 | 53% helix, 15% strand | P77704 |
| D | YdjI aldolase | protein | 256 | 52% helix, 16% strand | P77704 |
Ligands and binding sites
- ZN · Zinc ion · metal · 5 copies · chains A, B, C, D
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 521 | 0.70 | 0.80 | 42 | empty |
| 2 | 490 | 0.69 | 0.80 | 40 | empty |
| 3 | 76 | 0.41 | 0.80 | 20 | empty |
| 4 | 148 | 0.39 | 0.73 | 20 | empty |
| 5 | 151 | 0.38 | 0.73 | 23 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1570 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1557 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 447 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 433 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (oxidation).
Compared structures
- 6OFU · X-ray crystal structure of the ydji aldolase from escherichia COLI K12 · the same entry in another collection · chain D against D, TM-score 1.00
- P77704 · AlphaFold monomer V2.0 prediction for uncharacterized protein ydji (P77704) · 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 P77704
- Elsewhere: RCSB PDB 6OFU · PDBe 6OFU · UniProt P77704
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