MolNFT v1 · #151041 · protein
Crystal structure of MSMEG_1712 from mycobacterium smegmatis in complex with alpha-L-arabinofuranose
6HBM · ABC transporter periplasmic-binding protein ytfq: “Crystal structure of MSMEG_1712 from mycobacterium smegmatis in complex with alpha-L-arabinofuranose”. X-ray diffraction, 2 ligands (AHR, ZN), 7 pockets (best druggability 0.72).…
- PDB
- 6HBM
- Type
- protein
- Length
- 608 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ABC transporter periplasmic-binding protein ytfq
- UniProt
- A0QT50
- Ligands
- AHR, ZN
- Pockets
- 7 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | ABC transporter periplasmic-binding protein ytfq | protein | 304 | 44% helix, 21% strand | A0QT50 |
Ligands and binding sites
- AHR · alpha-L-arabinofuranose · sugar · 2 copies · chains A, B
- ZN · Zinc ion · metal · 12 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 53 | 0.72 | 0.99 | 14 | AHR |
| 2 | 364 | 0.64 | 0.79 | 33 | ZN |
| 3 | 396 | 0.64 | 0.79 | 43 | ZN |
| 4 | 148 | 0.62 | 0.85 | 30 | empty |
| 5 | 229 | 0.60 | 0.80 | 32 | ZN |
Interfaces
1 interface between chains.
- A–B · 977 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6HBM · Crystal structure of MSMEG_1712 from Mycobacterium smegmatis in complex with… · 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 A0QT50
- Elsewhere: RCSB PDB 6HBM · PDBe 6HBM · UniProt A0QT50
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