Research workbench
XaxAB pore complex from Xenorhabdus nematophila
Analyse XaxAB pore complex from Xenorhabdus nematophila in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GY6
- Type
- protein
- Length
- 9,139 residues
- Chains
- 26
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 4.0
- Source
- Xenorhabdus nematophila ATCC 19061
- Molecule
- XaxA; XaxB
- UniProt
- D3VB22, D3VB23
- Pockets
- 20 · best druggability 0.77
Structure
electron microscopy · resolution 4.0 · 2 distinct chains · 81% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, E, F, I, J, M, P, Q, R, S, T | XaxA | protein | 365 | 80% helix, 3% strand | D3VB22 |
| B, G, H, K, L, N, O, U, V, W, X, Y, Z | XaxB | protein | 338 | 82% helix, 0% strand | D3VB23 |
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 | 878 | 0.77 | 0.80 | 111 | empty |
| 2 | 1020 | 0.76 | 0.78 | 103 | empty |
| 3 | 698 | 0.76 | 0.81 | 97 | empty |
| 4 | 907 | 0.75 | 0.79 | 116 | empty |
| 5 | 945 | 0.74 | 0.78 | 112 | empty |
Interfaces
52 interfaces between chains.
- G–C · 3119 Ų buried · 28 hydrogen bonds · protein-protein
- W–Q · 3116 Ų buried · 28 hydrogen bonds · protein-protein
- Z–T · 3114 Ų buried · 28 hydrogen bonds · protein-protein
- H–D · 3113 Ų buried · 28 hydrogen bonds · protein-protein
- L–F · 3112 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 6GY6 · Xaxab pore complex from xenorhabdus nematophila · the same entry in another collection · chain B against B, 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 D3VB22
- Every structure of UniProt D3VB23
- Elsewhere: RCSB PDB 6GY6 · PDBe 6GY6 · UniProt D3VB22 · UniProt D3VB23
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