Research workbench
The crystal structure of the outer membrane transporter yddb from escherichia COLI
Analyse The crystal structure of the outer membrane transporter yddb from escherichia… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OFR
- Type
- protein
- Length
- 758 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tonb-dependent outer membrane receptor
- UniProt
- A0A024L3L4
- Ligands
- MG
- Pockets
- 9 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 7% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tonb-dependent outer membrane receptor | protein | 758 | 7% helix, 56% strand | A0A024L3L4 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A
- BOG · octyl beta-D-glucopyranoside · additive · 7 copies · chains A
- GOL · Glycerol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 453 | 0.86 | 0.93 | 61 | empty |
| 2 | 552 | 0.81 | 0.87 | 78 | GOL |
| 3 | 438 | 0.73 | 0.83 | 50 | empty |
| 4 | 493 | 0.68 | 0.79 | 60 | empty |
| 5 | 92 | 0.53 | 0.84 | 27 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6OFR · The crystal structure of the outer membrane transporter YddB from Escherichia coli · 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 A0A024L3L4
- Elsewhere: RCSB PDB 6OFR · PDBe 6OFR · UniProt A0A024L3L4
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