Research workbench
Crystal structure of lectin-like ox-LDL receptor 1 in complex with bi- 0115
Analyse Crystal structure of lectin-like ox-LDL receptor 1 in complex with bi- 0115 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TL9
- Type
- protein
- Length
- 1,038 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oxidized low-density lipoprotein receptor 1
- UniProt
- P78380
- Ligands
- NJT
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, E, F, G, H | Oxidized low-density lipoprotein receptor 1 | protein | 130 | 15% helix, 33% strand | P78380 |
| B, C | Oxidized low-density lipoprotein receptor 1 | protein | 129 | 16% helix, 33% strand | P78380 |
Ligands and binding sites
- NJT · 9-chloranyl-5-propyl-11~{H}-pyrido[2,3-B][1, 4]benzodiazepin-6-one · ligand · 4 copies · chains A, B, C, D, E, F, G, H
- GOL · Glycerol · additive · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 503 | 0.78 | 0.86 | 67 | empty |
| 2 | 384 | 0.75 | 0.85 | 50 | empty |
| 3 | 308 | 0.65 | 0.81 | 26 | NJT |
| 4 | 298 | 0.65 | 0.81 | 28 | NJT |
| 5 | 98 | 0.56 | 0.84 | 19 | empty |
Interfaces
16 interfaces between chains.
- C–D · 994 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 990 Ų buried · 12 hydrogen bonds · protein-protein
- G–H · 981 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 975 Ų buried · 10 hydrogen bonds · protein-protein
- C–H · 571 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide (disulfide).
Compared structures
- 6TL9 · Crystal structure of lectin-like ox-LDL receptor 1 in complex with bi-0115 · the same entry in another collection · chain H against H, TM-score 1.00
- P78380 · AlphaFold monomer V2.0 prediction for oxidized low-density lipoprotein receptor 1 (P78380) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P78380
- Elsewhere: RCSB PDB 6TL9 · PDBe 6TL9 · UniProt P78380
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