Research workbench
Ptex core complex in the resetting (compact) state
Analyse Ptex core complex in the resetting (compact) state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6E11
- Type
- protein
- Length
- 7,181 residues
- Chains
- 28
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Unknown (claw); Heat shock protein 101; Exported protein 2; Endogenous cargo polypeptide…
- UniProt
- Q8IIJ8, Q8IKC8, Q8ILA1
- Ligands
- AGS
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 14 distinct chains · 55% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| i | Unknown (claw) | protein | 46 | 74% helix, 0% strand | — |
| j | Unknown (claw) | protein | 55 | 69% helix, 0% strand | — |
| k | Unknown (claw) | protein | 60 | 70% helix, 0% strand | — |
| 1, 2, 3, 4 | Heat shock protein 101 | protein | 717 | 47% helix, 7% strand | Q8IIJ8 |
| 5, 6 | Heat shock protein 101 | protein | 716 | 46% helix, 7% strand | Q8IIJ8 |
| C, D, B, F | Exported protein 2 | protein | 209 | 67% helix, 3% strand | Q8IKC8 |
| 0 | Endogenous cargo polypeptide | protein | 6 | 0% helix, 0% strand | — |
| E | Exported protein 2 | protein | 210 | 66% helix, 1% strand | Q8IKC8 |
| d, c, b, a, g, f, e | Translocon component PTEX150 | protein | 156 | 39% helix, 4% strand | Q8ILA1 |
| A, G | Exported protein 2 | protein | 191 | 70% helix, 1% strand | Q8IKC8 |
| n | Unknown (claw) | protein | 36 | 94% helix, 0% strand | — |
| h | Unknown (claw) | protein | 47 | 79% helix, 0% strand | — |
| l | Unknown (claw) | protein | 53 | 77% helix, 0% strand | — |
| m | Unknown (claw) | protein | 58 | 69% 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 | 995 | 0.89 | 0.91 | 105 | empty |
| 2 | 894 | 0.89 | 0.91 | 133 | AGS |
| 3 | 1041 | 0.88 | 0.89 | 123 | empty |
| 4 | 871 | 0.88 | 0.90 | 108 | AGS |
| 5 | 990 | 0.87 | 0.88 | 87 | empty |
Interfaces
83 interfaces between chains.
- 1–2 · 5189 Ų buried · 50 hydrogen bonds · protein-protein
- 5–6 · 5167 Ų buried · 46 hydrogen bonds · protein-protein
- 2–3 · 4987 Ų buried · 64 hydrogen bonds · protein-protein
- 4–5 · 4923 Ų buried · 52 hydrogen bonds · protein-protein
- 3–4 · 3521 Ų buried · 31 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 covalent, 7 disulfide (covalent ligand, disulfide).
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 6E11 · PDBe 6E11 · UniProt Q8IIJ8 · UniProt Q8IKC8 · UniProt Q8ILA1
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