MolNFT v1 · #53904 · protein
Crystal structure of the ABN2 D171A mutant in complex with arabinotriose
2X8S · Endo-alpha-1,5-L-arabinanase: “Crystal structure of the ABN2 D171A mutant in complex with arabinotriose”. X-ray diffraction, 5 ligands (AHR, NA, CA), 11 pockets (best druggability 0.65). MolNFT v1 #53904 on GenesisL1: 3D structure…
- PDB
- 2X8S
- Type
- protein
- Length
- 886 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endo-alpha-1,5-L-arabinanase
- EC
- 3.2.1.99
- UniProt
- B3FRL6
- Ligands
- AHR, NA, CA, CL, PO4
- Pockets
- 11 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 5% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Endo-alpha-1,5-L-arabinanase (EC 3.2.1.99) | protein | 443 | 5% helix, 44% strand | B3FRL6 |
Ligands and binding sites
- AHR · alpha-L-arabinofuranose · sugar · 6 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains B
- CA · Calcium ion · metal · chains B
- CL · Chloride ion · ion · 3 copies · chains A, B
- PO4 · Phosphate ion · ion · chains B
- GOL · Glycerol · additive · 6 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 489 | 0.65 | 0.77 | 56 | empty |
| 2 | 296 | 0.64 | 0.80 | 25 | GOL |
| 3 | 313 | 0.62 | 0.79 | 26 | GOL |
| 4 | 340 | 0.56 | 0.75 | 48 | empty |
| 5 | 154 | 0.51 | 0.78 | 27 | AHR |
Interfaces
1 interface between chains.
- A–B · 616 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 2X8S · Crystal Structure of the Abn2 D171A mutant in complex with arabinotriose · 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 B3FRL6
- Elsewhere: RCSB PDB 2X8S · PDBe 2X8S · UniProt B3FRL6
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