MolNFT v1 · #152112 · protein
Microsomal triglyceride transfer protein
6I7S · Protein disulfide-isomerase: “Microsomal triglyceride transfer protein”. X-ray diffraction, 2 ligands (CA, SO4), 20 pockets (best druggability 0.87). MolNFT v1 #152112 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6I7S
- Type
- protein
- Length
- 2,648 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein disulfide-isomerase; Microsomal triglyceride transfer protein large subunit
- EC
- 5.3.4.1
- UniProt
- P07237, P55157
- Ligands
- CA, SO4
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein disulfide-isomerase (EC 5.3.4.1) | protein | 461 | 34% helix, 21% strand | P07237 |
| B | Protein disulfide-isomerase (EC 5.3.4.1) | protein | 462 | 34% helix, 21% strand | P07237 |
| G | Microsomal triglyceride transfer protein large subunit | protein | 863 | 32% helix, 36% strand | P55157 |
| H | Microsomal triglyceride transfer protein large subunit | protein | 862 | 31% helix, 36% strand | P55157 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 11 copies · chains B, H, G, A
- EDO · 1,2-ethanediol · additive · 19 copies · chains A, B, G, H
- PEG · Di(hydroxyethyl)ether · additive · 9 copies · chains B, H, G
- PGE · Triethylene glycol · additive · 6 copies · chains B, G, H
- PE5 · 3,6,9,12,15,18,21,24-octaoxahexacosan-1-ol · additive · 2 copies · chains G, H
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains G
- PE4 · 2-{2-[2-(2-{2-[2-(2-ethoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethanol · additive · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1161 | 0.87 | 0.88 | 103 | PE5, PEG |
| 2 | 1179 | 0.87 | 0.87 | 111 | PE5, PGE, EDO, PEG |
| 3 | 1061 | 0.80 | 0.82 | 111 | SO4, PEG |
| 4 | 1158 | 0.80 | 0.82 | 117 | PGE, EDO |
| 5 | 874 | 0.78 | 0.81 | 78 | empty |
Interfaces
3 interfaces between chains.
- B–H · 2216 Ų buried · 29 hydrogen bonds · protein-protein
- A–G · 2176 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 156 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6I7S · Microsomal triglyceride transfer protein · the same entry in another collection · chain H against H, TM-score 1.00
- P55157 · AlphaFold monomer V2.0 prediction for microsomal triglyceride transfer protein large… · a predicted model of the same protein · chain H against A, TM-score 0.97
- P07237 · AlphaFold monomer V2.0 prediction for protein disulfide-isomerase (P07237) · a predicted model of the same protein · chain A against A, TM-score 0.61
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 P07237
- Every structure of UniProt P55157
- Elsewhere: RCSB PDB 6I7S · PDBe 6I7S · UniProt P07237 · UniProt P55157
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