MolNFT v1 · #156249 · protein
Cryo-EM structure of phosphoketolase from bifidobacterium longum
6LXV: “Cryo-EM structure of phosphoketolase from bifidobacterium longum”. Electron microscopy, 2 ligands (TPP, CA), 20 pockets (best druggability 0.79). MolNFT v1 #156249 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6LXV
- Type
- protein
- Length
- 6,448 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoketolase
- EC
- 4.1.2.22
- UniProt
- D6D942
- Ligands
- TPP, CA
- Pockets
- 20 · best druggability 0.79
Structure
electron microscopy · 1 distinct chain · 43% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Phosphoketolase (EC 4.1.2.22) | protein | 806 | 43% helix, 15% strand | D6D942 |
Ligands and binding sites
- TPP · Thiamine diphosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- CA · Calcium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 819 | 0.79 | 0.82 | 114 | TPP, CA |
| 2 | 869 | 0.79 | 0.81 | 114 | TPP, CA |
| 3 | 874 | 0.79 | 0.81 | 113 | TPP, CA |
| 4 | 658 | 0.76 | 0.81 | 80 | TPP, CA |
| 5 | 647 | 0.76 | 0.82 | 78 | TPP, CA |
Interfaces
16 interfaces between chains.
- A–B · 5443 Ų buried · 117 hydrogen bonds · protein-protein
- E–F · 5430 Ų buried · 117 hydrogen bonds · protein-protein
- G–H · 5424 Ų buried · 117 hydrogen bonds · protein-protein
- C–D · 5423 Ų buried · 117 hydrogen bonds · protein-protein
- A–F · 545 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6LXV · Cryo-EM structure of phosphoketolase from Bifidobacterium longum · the same entry in another collection · 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 D6D942
- Elsewhere: RCSB PDB 6LXV · PDBe 6LXV · UniProt D6D942
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