MolNFT v1 · #152783 · protein
Structure of a substrate engaged seca-secy protein translocation machine
6ITC · Protein translocase subunit seca: “Structure of a substrate engaged seca-secy protein translocation machine”. Electron microscopy, 5 ligands (PGV, GYS, BEF), 20 pockets (best druggability 0.85). MolNFT v1 #152783 on GenesisL1: 3D…
- PDB
- 6ITC
- Type
- protein
- Length
- 1,738 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein translocase subunit seca; Protein translocase subunit secy; Protein translocase…
- UniProt
- P28366, A4IJK8, A4IJH4, P42212
- Ligands
- PGV, GYS, BEF, ADP, MG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 7 distinct chains · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein translocase subunit seca | protein | 765 | 52% helix, 10% strand | P28366 |
| Y | Protein translocase subunit secy | protein | 420 | 63% helix, 3% strand | A4IJK8 |
| E | Protein translocase subunit sece | protein | 58 | 81% helix, 2% strand | A4IJH4 |
| V | Nanobody | protein | 116 | 3% helix, 41% strand | — |
| B | Translocating peptide | protein | 43 | 49% helix, 9% strand | — |
| G | Green fluorescent protein | protein | 224 | 2% helix, 52% strand | P42212 |
| C | Nanobody | protein | 112 | 5% helix, 47% strand | — |
Ligands and binding sites
- PGV · (1R)-2-{[{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy) phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11E)-octadec-11-enoate · ligand · 2 copies · chains Y, E, B
- GYS · [(4Z)-2-(1-amino-2-hydroxyethyl)-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1H-imidazol-1-yl]acetic acid · ligand · chains G
- BEF · Beryllium trifluoride ion · ligand · chains A
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1010 | 0.85 | 0.86 | 111 | empty |
| 2 | 1043 | 0.83 | 0.84 | 101 | PGV |
| 3 | 178 | 0.83 | 0.97 | 30 | GYS |
| 4 | 746 | 0.78 | 0.82 | 74 | empty |
| 5 | 60 | 0.70 | 0.96 | 22 | empty |
Interfaces
9 interfaces between chains.
- A–Y · 2719 Ų buried · 17 hydrogen bonds · protein-protein
- Y–B · 1941 Ų buried · 10 hydrogen bonds · protein-protein
- Y–E · 1580 Ų buried · 7 hydrogen bonds · protein-protein
- Y–V · 923 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 765 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 2 cofactor (disulfide, chromophore).
Compared structures
- 6ITC · Structure of a substrate engaged SecA-SecY protein translocation machine · the same entry in another collection · chain C against C, TM-score 1.00
- P42212 · AlphaFold monomer V2.0 prediction for green fluorescent protein (P42212) · a predicted model of the same protein · chain G against A, TM-score 0.97
- P28366 · AlphaFold monomer V2.0 prediction for protein translocase subunit seca (P28366) · a predicted model of the same protein · chain A against A, TM-score 0.82
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 P28366
- Every structure of UniProt A4IJK8
- Every structure of UniProt A4IJH4
- Every structure of UniProt P42212
- Elsewhere: RCSB PDB 6ITC · PDBe 6ITC · UniProt P28366 · UniProt A4IJK8 · UniProt A4IJH4 · UniProt P42212
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.