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 v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Xaxa; Xaxb
- UniProt
- D3VB22, D3VB23
- Pockets
- 20 · best druggability 0.77
Structure
electron microscopy · 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 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 D3VB22
- Every structure of UniProt D3VB23
- Elsewhere: RCSB PDB 6GY6 · PDBe 6GY6 · UniProt D3VB22 · UniProt D3VB23
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