Research workbench
Crystal structure of arabinose isomerase from hybrid AI8 with adonitol
Analyse Crystal structure of arabinose isomerase from hybrid AI8 with adonitol in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7CYY
- 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, K0IGW6, Q2VMT2
- Ligands
- RB0, MN
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 6 distinct chains · 39% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-arabinose isomerase (EC 5.3.1.4) | protein | 496 | 38% helix, 23% strand | Q5KYP7, K0IGW6, Q2VMT2 |
| B | L-arabinose isomerase (EC 5.3.1.4) | protein | 494 | 40% helix, 23% strand | Q5KYP7, K0IGW6, Q2VMT2 |
| C | L-arabinose isomerase (EC 5.3.1.4) | protein | 497 | 39% helix, 23% strand | Q5KYP7, K0IGW6, Q2VMT2 |
| D | L-arabinose isomerase (EC 5.3.1.4) | protein | 490 | 39% helix, 23% strand | Q5KYP7, K0IGW6, Q2VMT2 |
| E | L-arabinose isomerase (EC 5.3.1.4) | protein | 492 | 39% helix, 23% strand | Q5KYP7, K0IGW6, Q2VMT2 |
| F | L-arabinose isomerase (EC 5.3.1.4) | protein | 493 | 41% helix, 23% strand | Q5KYP7, K0IGW6, Q2VMT2 |
Ligands and binding sites
- RB0 · D-ribitol · ligand · 6 copies · chains A, B, D, E, C, F
- MN · Manganese (II) ion · metal · 9 copies · chains A, E, B, C, D, F
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A, 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1191 | 0.85 | 0.86 | 143 | empty |
| 2 | 1112 | 0.82 | 0.83 | 124 | empty |
| 3 | 830 | 0.78 | 0.81 | 81 | empty |
| 4 | 453 | 0.76 | 0.85 | 54 | empty |
| 5 | 63 | 0.72 | 0.97 | 19 | RB0 |
Interfaces
10 interfaces between chains.
- A–D · 2517 Ų buried · 43 hydrogen bonds · protein-protein
- A–B · 2466 Ų buried · 38 hydrogen bonds · protein-protein
- B–D · 2462 Ų buried · 36 hydrogen bonds · protein-protein
- C–F · 2462 Ų buried · 37 hydrogen bonds · protein-protein
- D–E · 1207 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7CYY · Crystal structure of Arabinose isomerase from hybrid AI8 with Adonitol · 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 F 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
- Every structure of UniProt K0IGW6
- Every structure of UniProt Q2VMT2
- Elsewhere: RCSB PDB 7CYY · PDBe 7CYY · UniProt Q5KYP7 · UniProt K0IGW6 · UniProt Q2VMT2
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