MolNFT v1 · #105331 · protein
Crystal structure of thermophilic geobacillus kaustophilus L-arabinose isomerase in complex with L-arabitol
4R1Q: “Crystal structure of thermophilic geobacillus kaustophilus L-arabinose isomerase in complex with L-arabitol”. X-ray diffraction, 2 ligands (SST, MN), 20 pockets (best druggability 0.85). MolNFT v1 #105331 on GenesisL1: 3D structure…
- PDB
- 4R1Q
- Type
- protein
- Length
- 2,972 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-arabinose isomerase
- EC
- 5.3.1.4
- UniProt
- Q5KYP7
- Ligands
- SST, MN
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | L-arabinose isomerase (EC 5.3.1.4) | protein | 495 | 40% helix, 22% strand | Q5KYP7 |
| B, C | L-arabinose isomerase (EC 5.3.1.4) | protein | 495 | 41% helix, 22% strand | Q5KYP7 |
| D | L-arabinose isomerase (EC 5.3.1.4) | protein | 496 | 40% helix, 22% strand | Q5KYP7 |
| E | L-arabinose isomerase (EC 5.3.1.4) | protein | 496 | 41% helix, 22% strand | Q5KYP7 |
Ligands and binding sites
- SST · L-arabinitol · ligand · 6 copies · chains A, E, D, B, F, C
- MN · Manganese (II) ion · metal · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 916 | 0.85 | 0.87 | 115 | empty |
| 2 | 943 | 0.84 | 0.86 | 113 | empty |
| 3 | 786 | 0.80 | 0.83 | 101 | empty |
| 4 | 434 | 0.77 | 0.86 | 51 | empty |
| 5 | 579 | 0.76 | 0.82 | 60 | empty |
Interfaces
12 interfaces between chains.
- C–F · 2393 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 2383 Ų buried · 33 hydrogen bonds · protein-protein
- A–D · 2372 Ų buried · 29 hydrogen bonds · protein-protein
- B–F · 2350 Ų buried · 33 hydrogen bonds · protein-protein
- D–E · 2346 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 4R1Q · Crystal Structure of Thermophilic Geobacillus kaustophilus L-Arabinose isomerase in… · the same entry in another collection · chain D against D, TM-score 1.00
- Q5KYP7 · AlphaFold monomer V2.0 prediction for L-arabinose isomerase (Q5KYP7) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q5KYP7
- Elsewhere: RCSB PDB 4R1Q · PDBe 4R1Q · UniProt Q5KYP7
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