Research workbench
Trypanosoma cruzi - BDF2, TCCLB.506553.20, solved with bromosporine
Analyse Trypanosoma cruzi - BDF2, TCCLB.506553.20, solved with bromosporine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NIM
- Type
- protein
- Length
- 226 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bromodomain factor 2 protein
- UniProt
- A0A2V2V5V1
- Ligands
- BMF, UNX, SO4
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 57% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Bromodomain factor 2 protein | protein | 113 | 57% helix, 0% strand | A0A2V2V5V1 |
Ligands and binding sites
- BMF · Bromosporine · ligand · chains B
- UNX · Unknown atom or ion · ion · 5 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 463 | 0.72 | 0.82 | 52 | empty |
| 2 | 88 | 0.48 | 0.82 | 20 | BMF, UNX |
| 3 | 75 | 0.46 | 0.82 | 18 | empty |
| 4 | 91 | 0.39 | 0.77 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 658 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 6NIM · Trypanosoma cruzi - BDF2, TcCLB.506553.20, solved with bromosporine · 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 A0A2V2V5V1
- Elsewhere: RCSB PDB 6NIM · PDBe 6NIM · UniProt A0A2V2V5V1
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