MolNFT v1 · #170473 · protein
Mycobacterium thermoresistibile GYRB21 in complex with REDX03863
6Y8N · DNA gyrase subunit B: “Mycobacterium thermoresistibile GYRB21 in complex with REDX03863”. X-ray diffraction, 2 ligands (OGH, ZN), 4 pockets (best druggability 0.79). MolNFT v1 #170473 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6Y8N
- Type
- protein
- Length
- 360 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
- OGH, ZN
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA gyrase subunit B (EC 5.6.2.2) | protein | 183 | 33% helix, 31% strand | A0A117ILT2 |
| B | DNA gyrase subunit B (EC 5.6.2.2) | protein | 177 | 33% helix, 31% strand | A0A117ILT2 |
Ligands and binding sites
- OGH · 4-[(1~{S},5~{R})-6-azanyl-3-azabicyclo[3.1.0]hexan-3-yl]-6-fluoranyl-~{N}-methyl-2-(2-methylpyrimidin-5-yl)oxy-9~{H}-pyrimido[4,5-b]indol-8-amine · 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
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 471 | 0.79 | 0.86 | 58 | empty |
| 2 | 192 | 0.69 | 0.87 | 28 | OGH |
| 3 | 180 | 0.68 | 0.87 | 25 | OGH |
| 4 | 86 | 0.38 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1094 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 6Y8N · Mycobacterium thermoresistibile GyrB21 in complex with Redx03863 · 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 6Y8N · PDBe 6Y8N · UniProt A0A117ILT2
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