Research workbench
Crystal structure of thermophilic geobacillus kaustophilus L-arabinose isomerase with MN2+
Analyse Crystal structure of thermophilic geobacillus kaustophilus L-arabinose… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4R1P
- Type
- protein
- Length
- 2,962 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
- MN
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | L-arabinose isomerase (EC 5.3.1.4) | protein | 494 | 41% helix, 23% strand | Q5KYP7 |
| B | L-arabinose isomerase (EC 5.3.1.4) | protein | 492 | 41% helix, 23% strand | Q5KYP7 |
| C, E | L-arabinose isomerase (EC 5.3.1.4) | protein | 495 | 41% helix, 23% strand | Q5KYP7 |
| F | L-arabinose isomerase (EC 5.3.1.4) | protein | 492 | 41% helix, 23% strand | Q5KYP7 |
Ligands and binding sites
- 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 958 | 0.82 | 0.83 | 112 | empty |
| 2 | 644 | 0.82 | 0.87 | 86 | empty |
| 3 | 770 | 0.81 | 0.84 | 85 | empty |
| 4 | 551 | 0.79 | 0.85 | 79 | empty |
| 5 | 336 | 0.74 | 0.85 | 43 | empty |
Interfaces
12 interfaces between chains.
- A–E · 2392 Ų buried · 28 hydrogen bonds · protein-protein
- C–F · 2369 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 2360 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 2359 Ų buried · 29 hydrogen bonds · protein-protein
- D–F · 2353 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 4R1P · Crystal Structure of Thermophilic Geobacillus kaustophilus L-Arabinose isomerase with Mn2+ · the same entry in another collection · chain F against F, TM-score 1.00
- Q5KYP7 · AlphaFold monomer V2.0 prediction for L-arabinose isomerase (Q5KYP7) · a predicted model of the same protein · chain C 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 4R1P · PDBe 4R1P · UniProt Q5KYP7
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