Research workbench
Crystal structure of the catalytic domain of XYNA1 from paenibacillus sp. jdr-2
Analyse Crystal structure of the catalytic domain of XYNA1 from paenibacillus sp. jdr-2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RO8
- Type
- protein
- Length
- 2,424 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endo-1,4-beta-xylanase
- EC
- 3.2.1.8
- UniProt
- C6CRV0
- Ligands
- MG, CL
- Pockets
- 18 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, F, G, H | Endo-1,4-beta-xylanase (EC 3.2.1.8) | protein | 304 | 46% helix, 21% strand | C6CRV0 |
| C | Endo-1,4-beta-xylanase (EC 3.2.1.8) | protein | 302 | 46% helix, 21% strand | C6CRV0 |
| D, E | Endo-1,4-beta-xylanase (EC 3.2.1.8) | protein | 301 | 47% helix, 21% strand | C6CRV0 |
Ligands and binding sites
- MG · Magnesium ion · metal · 11 copies · chains A, E, B, C, G, D, F, H
- CL · Chloride ion · ion · 9 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 657 | 0.80 | 0.85 | 117 | empty |
| 2 | 1167 | 0.79 | 0.81 | 86 | MG |
| 3 | 742 | 0.77 | 0.81 | 68 | empty |
| 4 | 746 | 0.70 | 0.77 | 52 | empty |
| 5 | 706 | 0.70 | 0.77 | 48 | empty |
Interfaces
15 interfaces between chains.
- A–C · 1121 Ų buried · 7 hydrogen bonds · protein-protein
- F–G · 1110 Ų buried · 13 hydrogen bonds · protein-protein
- B–F · 570 Ų buried · 14 hydrogen bonds · protein-protein
- D–H · 538 Ų buried · 12 hydrogen bonds · protein-protein
- C–G · 472 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3RO8 · Crystal structure of the catalytic domain of XynA1 from Paenibacillus sp. JDR-2 · the same entry in another collection · chain D against D, TM-score 1.00
- C6CRV0 · AlphaFold monomer V2.0 prediction for endo-1,4-beta-xylanase a (C6CRV0) · a predicted model of the same protein · chain D against A, TM-score 0.98
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 C6CRV0
- Elsewhere: RCSB PDB 3RO8 · PDBe 3RO8 · UniProt C6CRV0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.