Research workbench
Paxb from photorhabdus luminescens
Analyse Paxb from photorhabdus luminescens in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6EK4
- Type
- protein
- Length
- 1,317 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Paxb
- Ligands
- NA
- Pockets
- 18 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 80% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Paxb | protein | 342 | 80% helix, 1% strand | — |
| B | Paxb | protein | 313 | 81% helix, 1% strand | — |
| C | Paxb | protein | 330 | 81% helix, 1% strand | — |
| D | Paxb | protein | 332 | 79% helix, 1% strand | — |
Ligands and binding sites
- NA · Sodium ion · metal · 4 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 449 | 0.79 | 0.87 | 75 | empty |
| 2 | 496 | 0.77 | 0.85 | 63 | NA |
| 3 | 573 | 0.75 | 0.82 | 58 | NA |
| 4 | 307 | 0.74 | 0.87 | 39 | empty |
| 5 | 508 | 0.72 | 0.81 | 61 | NA |
Interfaces
6 interfaces between chains.
- B–C · 1466 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 1417 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 783 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 708 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 661 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6EK4 · PaxB from Photorhabdus luminescens · 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
- Elsewhere: RCSB PDB 6EK4 · PDBe 6EK4
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