MolNFT v1 · #68043 · protein + RNA
Structure of the secy protein translocation channel in action
3J46 · Protein translocase subunit secy: “Structure of the secy protein translocation channel in action”. Electron microscopy, 2 ligands (ACE, NH2), 20 pockets (best druggability 0.85). MolNFT v1 #68043 on GenesisL1: 3D structure, binding…
- PDB
- 3J46
- Type
- protein + RNA
- Length
- 1,558 residues
- Chains
- 14
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein translocase subunit secy; Preprotein translocase subunit sece; Protein-export…
- UniProt
- P0AGA2, P0AG96, P0AG99, P0A7L0, P0ADZ0, P60624, P0A7M6
- Ligands
- ACE, NH2
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 14 distinct chains · 45% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| y | Protein translocase subunit secy | protein | 435 | 72% helix, 1% strand | P0AGA2 |
| E | Preprotein translocase subunit sece | protein | 54 | 87% helix, 0% strand | P0AG96 |
| G | Protein-export membrane protein secg | protein | 65 | 66% helix, 0% strand | P0AG99 |
| n | NC100 | protein | 100 | 15% helix, 1% strand | — |
| p | P-tRNA | rna | 76 | — | — |
| a | A-tRNA | rna | 76 | — | — |
| 5 | 50S ribosomal protein L1 | protein | 234 | 21% helix, 18% strand | P0A7L0 |
| T | 50S ribosomal protein L23P | protein | 100 | 12% helix, 23% strand | P0ADZ0 |
| U | 50S ribosomal protein L24P | protein | 103 | 0% helix, 33% strand | P60624 |
| Y | 50S ribosomal protein L29P | protein | 63 | 71% helix, 0% strand | P0A7M6 |
| 1 | 23S ribosomal RNA | rna | 63 | — | — |
| 2 | 23S ribosomal RNA | rna | 36 | — | — |
| 3 | 23S ribosomal RNA | rna | 44 | — | — |
| 4 | 23S ribosomal RNA | rna | 109 | — | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 4 copies · chains y, E, n, G
- NH2 · Amino group · ion · 3 copies · chains y, E, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 886 | 0.85 | 0.87 | 83 | ACE |
| 2 | 512 | 0.84 | 0.90 | 63 | empty |
| 3 | 386 | 0.82 | 0.90 | 41 | empty |
| 4 | 188 | 0.80 | 0.96 | 31 | empty |
| 5 | 142 | 0.75 | 0.93 | 31 | empty |
Interfaces
25 interfaces between chains.
- y–n · 3440 Ų buried · 25 hydrogen bonds · protein-protein
- 5–4 · 2992 Ų buried · 84 hydrogen bonds · protein-nucleic
- y–E · 2082 Ų buried · 9 hydrogen bonds · protein-protein
- y–G · 2020 Ų buried · 19 hydrogen bonds · protein-protein
- Y–1 · 1133 Ų buried · 20 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 covalent, 1 disulfide, 1 modified (covalent ligand, disulfide, nucleotide modification).
Compared structures
- 3J46 · Structure of the SecY protein translocation channel in action · the same entry in another collection · chain 4 against 4, 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 P0AGA2
- Every structure of UniProt P0AG96
- Every structure of UniProt P0AG99
- Every structure of UniProt P0A7L0
- Every structure of UniProt P0ADZ0
- Every structure of UniProt P60624
- Every structure of UniProt P0A7M6
- Elsewhere: RCSB PDB 3J46 · PDBe 3J46 · UniProt P0AGA2 · UniProt P0AG96 · UniProt P0AG99 · UniProt P0A7L0 · UniProt P0ADZ0 · UniProt P60624 · UniProt P0A7M6
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.