MolNFT v1 · #121182 · protein
The structure of the kdo-capped saccharide binding subunit of the O-12 specific ABC transporter, wzt
5HNO · ABC type transport system putative ATP binding protein: “The structure of the kdo-capped saccharide binding subunit of the O-12 specific ABC transporter, wzt”. X-ray diffraction, 1 ligand (CL), 4 pockets (best druggability 0.49).…
- PDB
- 5HNO
- Type
- protein
- Length
- 498 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ABC type transport system putative ATP binding protein
- UniProt
- Q6U8B1
- Ligands
- CL
- Pockets
- 4 · best druggability 0.49
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ABC type transport system putative ATP binding protein | protein | 164 | 9% helix, 52% strand | Q6U8B1 |
| B | ABC type transport system putative ATP binding protein | protein | 168 | 8% helix, 52% strand | Q6U8B1 |
| C | ABC type transport system putative ATP binding protein | protein | 166 | 8% helix, 49% strand | Q6U8B1 |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains A, C
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 | 124 | 0.49 | 0.80 | 26 | CL |
| 2 | 74 | 0.31 | 0.75 | 21 | empty |
| 3 | 58 | 0.30 | 0.75 | 18 | empty |
| 4 | 52 | 0.26 | 0.74 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1598 Ų buried · 34 hydrogen bonds · protein-protein
- A–C · 438 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 141 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5HNO · The structure of the kdo-capped saccharide binding subunit of the O-12 specific ABC… · 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 Q6U8B1
- Elsewhere: RCSB PDB 5HNO · PDBe 5HNO · UniProt Q6U8B1
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