Research workbench
Crystal structure of arabinose isomerase from hybrid AI10
Analyse Crystal structure of arabinose isomerase from hybrid AI10 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7CXO
- Type
- protein
- Length
- 2,961 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
- K0IGW6, Q5KYP7, P58538
- Ligands
- MN
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | L-arabinose isomerase (EC 5.3.1.4) | protein | 494 | 40% helix, 23% strand | K0IGW6, Q5KYP7, P58538 |
| B, E | L-arabinose isomerase (EC 5.3.1.4) | protein | 496 | 41% helix, 22% strand | K0IGW6, Q5KYP7, P58538 |
| C | L-arabinose isomerase (EC 5.3.1.4) | protein | 486 | 38% helix, 22% strand | K0IGW6, Q5KYP7, P58538 |
| F | L-arabinose isomerase (EC 5.3.1.4) | protein | 495 | 39% helix, 23% strand | K0IGW6, Q5KYP7, P58538 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 6 copies · chains A, B, C, D, E, F
- GOL · Glycerol · additive · 5 copies · chains A, E, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1055 | 0.82 | 0.83 | 122 | empty |
| 2 | 514 | 0.76 | 0.84 | 59 | empty |
| 3 | 538 | 0.76 | 0.83 | 61 | empty |
| 4 | 256 | 0.71 | 0.86 | 40 | empty |
| 5 | 353 | 0.69 | 0.82 | 37 | empty |
Interfaces
12 interfaces between chains.
- D–F · 2420 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 2387 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 2386 Ų buried · 30 hydrogen bonds · protein-protein
- E–F · 2350 Ų buried · 29 hydrogen bonds · protein-protein
- D–E · 2339 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 7CXO · Crystal structure of Arabinose isomerase from hybrid AI10 · the same entry in another collection · chain B against B, TM-score 1.00
- P58538 · AlphaFold monomer V2.0 prediction for L-arabinose isomerase (P58538) · a predicted model of the same protein · chain C against A, TM-score 0.98
- Q5KYP7 · AlphaFold monomer V2.0 prediction for L-arabinose isomerase (Q5KYP7) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 K0IGW6
- Every structure of UniProt Q5KYP7
- Every structure of UniProt P58538
- Elsewhere: RCSB PDB 7CXO · PDBe 7CXO · UniProt K0IGW6 · UniProt Q5KYP7 · UniProt P58538
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