Research workbench
Crystal structure of LDBPK_091320 with inhibitor bound
Analyse Crystal structure of LDBPK_091320 with inhibitor bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BYA
- Type
- protein
- Length
- 472 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein
- UniProt
- E9BA17
- Ligands
- 2LO, UNX
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 64% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein | protein | 118 | 64% helix, 0% strand | E9BA17 |
| B | Uncharacterized protein | protein | 120 | 64% helix, 0% strand | E9BA17 |
| C | Uncharacterized protein | protein | 117 | 65% helix, 0% strand | E9BA17 |
| D | Uncharacterized protein | protein | 117 | 63% helix, 0% strand | E9BA17 |
Ligands and binding sites
- 2LO · 2-[2-(3-chloro-4-methoxyphenyl)ethyl]-5-(3,5-dimethyl-1,2-oxazol-4-yl)-1-[(2S)-2-(morpholin-4-yl)propyl]-1H-benzimidazole · ligand · 4 copies · chains A, B, C, D
- UNX · Unknown atom or ion · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 883 | 0.75 | 0.79 | 56 | empty |
| 2 | 576 | 0.70 | 0.78 | 50 | 2LO |
| 3 | 104 | 0.56 | 0.84 | 20 | 2LO |
| 4 | 108 | 0.53 | 0.83 | 20 | empty |
| 5 | 103 | 0.53 | 0.83 | 21 | 2LO |
Interfaces
5 interfaces between chains.
- A–C · 660 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 636 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 628 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 149 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 115 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6BYA · Crystal structure of LdBPK_091320 with inhibitor bound · 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 E9BA17
- Elsewhere: RCSB PDB 6BYA · PDBe 6BYA · UniProt E9BA17
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