Research workbench
Crystal structure of endo-1,5-alpha-L-arabinanase from thermotoga petrophila rku-1
Analyse Crystal structure of endo-1,5-alpha-L-arabinanase from thermotoga petrophila… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KC7
- Type
- protein
- Length
- 1,331 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 0.72
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 | 433 | 6% helix, 45% strand | A5IKD4 |
Ligands and binding sites
- CA · Calcium ion · metal · 3 copies · chains A, B, C
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 837 | 0.72 | 0.77 | 88 | empty |
| 2 | 285 | 0.58 | 0.77 | 23 | empty |
| 3 | 243 | 0.57 | 0.78 | 21 | empty |
| 4 | 300 | 0.56 | 0.76 | 39 | empty |
| 5 | 147 | 0.54 | 0.81 | 25 | PEG |
Interfaces
3 interfaces between chains.
- A–C · 400 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 312 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 82 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4KC7 · Crystal Structure of Endo-1,5-alpha-L-arabinanase from Thermotoga petrophila RKU-1 · 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 B 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 4KC7 · PDBe 4KC7 · UniProt A5IKD4
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