MolNFT v1 · #103286 · protein
Bombyx mori lipoprotein 6
4PC4 · 30K lipoprotein: “Bombyx mori lipoprotein 6”. X-ray diffraction, 3 pockets (best druggability 0.74). MolNFT v1 #103286 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4PC4
- Type
- protein
- Length
- 1,193 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 30K lipoprotein
- UniProt
- A7LIK7
- Pockets
- 3 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | 30K lipoprotein | protein | 238 | 31% helix, 32% strand | A7LIK7 |
| C | 30K lipoprotein | protein | 240 | 31% helix, 32% strand | A7LIK7 |
| E | 30K lipoprotein | protein | 239 | 31% helix, 32% strand | A7LIK7 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B, C
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 4 copies · chains A, B, C
- IPA · Isopropyl alcohol · additive · 3 copies · chains C
- PEG · Di(hydroxyethyl)ether · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 930 | 0.74 | 0.78 | 91 | MES |
| 2 | 950 | 0.71 | 0.76 | 84 | MES |
| 3 | 298 | 0.54 | 0.76 | 51 | empty |
Interfaces
6 interfaces between chains.
- A–B · 575 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 562 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 542 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 191 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 38 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 4PC4 · Bombyx mori lipoprotein 6 · 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 A7LIK7
- Elsewhere: RCSB PDB 4PC4 · PDBe 4PC4 · UniProt A7LIK7
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