MolNFT v1 · #170471 · protein
Mycobacterium thermoresistibile GYRB21 in complex with novobiocin
6Y8L · DNA gyrase subunit B: “Mycobacterium thermoresistibile GYRB21 in complex with novobiocin”. X-ray diffraction, 2 ligands (NOV, ZN), 5 pockets (best druggability 0.78). MolNFT v1 #170471 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6Y8L
- Type
- protein
- Length
- 363 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA gyrase subunit B
- EC
- 5.6.2.2
- UniProt
- A0A117ILT2
- Ligands
- NOV, ZN
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA gyrase subunit B (EC 5.6.2.2) | protein | 184 | 33% helix, 30% strand | A0A117ILT2 |
| B | DNA gyrase subunit B (EC 5.6.2.2) | protein | 179 | 33% helix, 30% strand | A0A117ILT2 |
Ligands and binding sites
- NOV · Novobiocin · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 6 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 406 | 0.78 | 0.87 | 47 | empty |
| 2 | 201 | 0.73 | 0.89 | 27 | NOV |
| 3 | 233 | 0.70 | 0.86 | 28 | NOV |
| 4 | 71 | 0.34 | 0.76 | 11 | empty |
| 5 | 72 | 0.32 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1088 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 6Y8L · Mycobacterium thermoresistibile GyrB21 in complex with novobiocin · 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 A0A117ILT2
- Elsewhere: RCSB PDB 6Y8L · PDBe 6Y8L · UniProt A0A117ILT2
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