Research workbench
Cryo-EM structure of xenorhabdus nematophila XPTA1
Analyse Cryo-EM structure of xenorhabdus nematophila XPTA1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RW8
- Type
- protein
- Length
- 11,685 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- A component of insecticidal toxin complex (tc)
- UniProt
- A0A0R4FN93
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 1 distinct chain · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | A component of insecticidal toxin complex (tc) | protein | 2337 | 43% helix, 16% strand | A0A0R4FN93 |
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 | 794 | 0.85 | 0.88 | 81 | empty |
| 2 | 1102 | 0.85 | 0.86 | 104 | empty |
| 3 | 813 | 0.85 | 0.87 | 96 | empty |
| 4 | 1171 | 0.85 | 0.86 | 157 | empty |
| 5 | 1063 | 0.84 | 0.85 | 120 | empty |
Interfaces
10 interfaces between chains.
- A–B · 11646 Ų buried · 114 hydrogen bonds · protein-protein
- B–C · 11640 Ų buried · 113 hydrogen bonds · protein-protein
- A–E · 11638 Ų buried · 113 hydrogen bonds · protein-protein
- D–E · 11637 Ų buried · 115 hydrogen bonds · protein-protein
- C–D · 11623 Ų buried · 113 hydrogen bonds · protein-protein
Compared structures
- 6RW8 · Cryo-EM structure of Xenorhabdus nematophila XptA1 · the same entry in another collection · chain A against A, 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 A0A0R4FN93
- Elsewhere: RCSB PDB 6RW8 · PDBe 6RW8 · UniProt A0A0R4FN93
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