Research workbench
Ptex core complex in the engaged (extended) state
Analyse Ptex core complex in the engaged (extended) state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6E10
- Type
- protein
- Length
- 7,170 residues
- Chains
- 28
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heat shock protein 101; Exported protein 2; Translocon component PTEX150; Endogenous…
- UniProt
- Q8IIJ8, Q8IKC8, Q8ILA1
- Ligands
- AGS
- Pockets
- 20 · best druggability 0.90
Structure
electron microscopy · 15 distinct chains · 56% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1 | Heat shock protein 101 | protein | 719 | 48% helix, 7% strand | Q8IIJ8 |
| 2, 3, 4, 6 | Heat shock protein 101 | protein | 718 | 54% helix, 9% strand | Q8IIJ8 |
| 5 | Heat shock protein 101 | protein | 711 | 53% helix, 11% strand | Q8IIJ8 |
| B, F, E, D, C | Exported protein 2 | protein | 209 | 66% helix, 3% strand | Q8IKC8 |
| a, g, f, e, d, c, b | Translocon component PTEX150 | protein | 156 | 33% helix, 7% strand | Q8ILA1 |
| A | Exported protein 2 | protein | 189 | 67% helix, 2% strand | Q8IKC8 |
| G | Exported protein 2 | protein | 195 | 68% helix, 2% strand | Q8IKC8 |
| 0 | Endogenous cargo polypeptide | protein | 15 | 0% helix, 33% strand | — |
| h | Translocon component PTEX150 | protein | 50 | 74% helix, 0% strand | Q8ILA1 |
| i | Unknown (claw) | protein | 46 | 74% helix, 0% strand | — |
| j | Unknown (claw) | protein | 53 | 79% helix, 0% strand | — |
| k | Unknown (claw) | protein | 58 | 69% helix, 0% strand | — |
| l | Unknown (claw) | protein | 57 | 70% helix, 0% strand | — |
| m | Unknown (claw) | protein | 33 | 94% helix, 0% strand | — |
| n | Unknown (claw) | protein | 35 | 94% helix, 0% strand | — |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 12 copies · chains 1, 2, 3, 4, 5, 6
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 901 | 0.90 | 0.92 | 123 | AGS |
| 2 | 1083 | 0.88 | 0.89 | 108 | empty |
| 3 | 737 | 0.88 | 0.91 | 88 | AGS |
| 4 | 1103 | 0.87 | 0.88 | 123 | AGS |
| 5 | 751 | 0.86 | 0.89 | 106 | AGS |
Interfaces
82 interfaces between chains.
- 2–3 · 5510 Ų buried · 50 hydrogen bonds · protein-protein
- 3–4 · 5490 Ų buried · 56 hydrogen bonds · protein-protein
- 4–5 · 5345 Ų buried · 55 hydrogen bonds · protein-protein
- 1–2 · 5179 Ų buried · 52 hydrogen bonds · protein-protein
- 5–6 · 4728 Ų buried · 41 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 4 isopeptide, 1 covalent (disulfide, isopeptide, covalent ligand).
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 Q8IIJ8
- Every structure of UniProt Q8IKC8
- Every structure of UniProt Q8ILA1
- Elsewhere: RCSB PDB 6E10 · PDBe 6E10 · UniProt Q8IIJ8 · UniProt Q8IKC8 · UniProt Q8ILA1
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