Research workbench
EM fitted model of bacterial holo-translocon
Analyse EM fitted model of bacterial holo-translocon in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MG3
- Type
- protein
- Length
- 1,698 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein translocase subunit secy; Protein translocase subunit sece; Protein-export…
- UniProt
- P0AGA2, P0AG96, P0AG99, P0AG90, P0AG93, P25714
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 6 distinct chains · 43% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| Y | Protein translocase subunit secy | protein | 443 | 44% helix, 1% strand | P0AGA2 |
| E | Protein translocase subunit sece | protein | 65 | 71% helix, 0% strand | P0AG96 |
| G | Protein-export membrane protein secg | protein | 32 | 34% helix, 0% strand | P0AG99 |
| D | Protein translocase subunit secd | protein | 414 | 47% helix, 12% strand | P0AG90 |
| F | Protein translocase subunit secf | protein | 289 | 60% helix, 10% strand | P0AG93 |
| C | Membrane protein insertase yidc | protein | 455 | 23% helix, 29% strand | P25714 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 898 | 0.86 | 0.88 | 87 | empty |
| 2 | 764 | 0.81 | 0.84 | 74 | empty |
| 3 | 414 | 0.76 | 0.85 | 58 | empty |
| 4 | 361 | 0.76 | 0.86 | 56 | empty |
| 5 | 387 | 0.75 | 0.85 | 37 | empty |
Interfaces
12 interfaces between chains.
- D–F · 3300 Ų buried · 45 hydrogen bonds · protein-protein
- Y–C · 2506 Ų buried · 29 hydrogen bonds · protein-protein
- Y–E · 2150 Ų buried · 10 hydrogen bonds · protein-protein
- F–C · 1599 Ų buried · 8 hydrogen bonds · protein-protein
- Y–G · 1146 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 5MG3 · EM fitted model of bacterial holo-translocon · the same entry in another collection · chain C against C, TM-score 1.00
- P0AG93 · AlphaFold monomer V2.0 prediction for protein translocase subunit secf (P0AG93) · a predicted model of the same protein · chain F against A, TM-score 0.72
- P0AGA2 · AlphaFold monomer V2.0 prediction for protein translocase subunit secy (P0AGA2) · a predicted model of the same protein · chain Y against A, TM-score 0.60
- P25714 · AlphaFold monomer V2.0 prediction for membrane protein insertase yidc (P25714) · a predicted model of the same protein · chain C against A, TM-score 0.53
- P0AG96 · AlphaFold monomer V2.0 prediction for protein translocase subunit sece (P0AG96) · a predicted model of the same protein · chain E against A, TM-score 0.44
- P0AG99 · AlphaFold monomer V2.0 prediction for protein-export membrane protein secg (P0AG99) · a predicted model of the same protein · chain G against A, TM-score 0.42
- P0AG90 · AlphaFold monomer V2.0 prediction for protein translocase subunit secd (P0AG90) · a predicted model of the same protein · chain D against A, TM-score 0.39
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 P0AG90
- Every structure of UniProt P0AG93
- Every structure of UniProt P25714
- Elsewhere: RCSB PDB 5MG3 · PDBe 5MG3 · UniProt P0AGA2 · UniProt P0AG96 · UniProt P0AG99 · UniProt P0AG90 · UniProt P0AG93 · UniProt P25714
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