MolNFT v1 · #154696 · protein
Xylanase J from bacillus sp. strain 41M-1
6KJL · Endo-1,4-beta-xylanase: “Xylanase J from bacillus sp. strain 41M-1”. X-ray diffraction, 1 ligand (CA), 6 pockets (best druggability 0.72). MolNFT v1 #154696 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6KJL
- Type
- protein
- Length
- 655 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endo-1,4-beta-xylanase
- EC
- 3.2.1.8
- UniProt
- Q9RC94
- Ligands
- CA
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 60% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endo-1,4-beta-xylanase (EC 3.2.1.8) | protein | 328 | 5% helix, 60% strand | Q9RC94 |
| B | Endo-1,4-beta-xylanase (EC 3.2.1.8) | protein | 327 | 5% helix, 61% strand | Q9RC94 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B
- GOL · Glycerol · additive · 10 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 6 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 830 | 0.72 | 0.77 | 97 | EPE, GOL, MPD |
| 2 | 433 | 0.67 | 0.79 | 62 | MPD, GOL |
| 3 | 543 | 0.63 | 0.76 | 47 | MPD |
| 4 | 70 | 0.42 | 0.80 | 16 | empty |
| 5 | 69 | 0.38 | 0.79 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1521 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 6KJL · Xylanase J from Bacillus sp. strain 41M-1 · 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 Q9RC94
- Elsewhere: RCSB PDB 6KJL · PDBe 6KJL · UniProt Q9RC94
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