MolNFT v1 · #97385 · protein
Crystal structure of endo-1,5-alpha-L-arabinanase from thermotoga petrophila rku-1 in complex with tris
4KC8 · Glycoside hydrolase, family 43: “Crystal structure of endo-1,5-alpha-L-arabinanase from thermotoga petrophila rku-1 in complex with tris”. X-ray diffraction, 1 ligand (CA), 14 pockets (best druggability 0.68). MolNFT v1 #97385 on…
- PDB
- 4KC8
- Type
- protein
- Length
- 1,341 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycoside hydrolase, family 43
- EC
- 3.2.1.99
- UniProt
- A5IKD4
- Ligands
- CA
- Pockets
- 14 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glycoside hydrolase, family 43 (EC 3.2.1.99) | protein | 449 | 6% helix, 45% strand | A5IKD4 |
| C | Glycoside hydrolase, family 43 (EC 3.2.1.99) | protein | 443 | 6% helix, 46% strand | A5IKD4 |
Ligands and binding sites
- CA · Calcium ion · metal · 3 copies · chains A, B, C
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 450 | 0.68 | 0.80 | 47 | empty |
| 2 | 749 | 0.68 | 0.75 | 74 | empty |
| 3 | 273 | 0.58 | 0.77 | 19 | empty |
| 4 | 151 | 0.57 | 0.82 | 25 | TRS |
| 5 | 181 | 0.56 | 0.80 | 30 | TRS |
Interfaces
3 interfaces between chains.
- B–C · 475 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 328 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 91 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4KC8 · Crystal Structure of Endo-1,5-alpha-L-arabinanase from Thermotoga petrophila RKU-1 in… · the same entry in another collection · chain A against A, TM-score 1.00
- A5IKD4 · AlphaFold monomer V2.0 prediction for extracellular endo- alpha-(1->5)-L-arabinanase… · a predicted model of the same protein · 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 A5IKD4
- Elsewhere: RCSB PDB 4KC8 · PDBe 4KC8 · UniProt A5IKD4
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