Research workbench
Crystal structure of arabinose isomerase from hyper thermophilic bacterium thermotoga maritima (tmai) wt
Analyse Crystal structure of arabinose isomerase from hyper thermophilic bacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7CWV
- Type
- protein
- Length
- 5,927 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-arabinose isomerase
- EC
- 5.3.1.4
- UniProt
- Q9WYB3
- Ligands
- MN
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-arabinose isomerase (EC 5.3.1.4) | protein | 491 | 38% helix, 21% strand | Q9WYB3 |
| B | L-arabinose isomerase (EC 5.3.1.4) | protein | 494 | 38% helix, 21% strand | Q9WYB3 |
| C | L-arabinose isomerase (EC 5.3.1.4) | protein | 487 | 38% helix, 21% strand | Q9WYB3 |
| D, E, F, G, H, I, J, K, L | L-arabinose isomerase (EC 5.3.1.4) | protein | 495 | 38% helix, 21% strand | Q9WYB3 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- GOL · Glycerol · additive · 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1088 | 0.85 | 0.86 | 87 | empty |
| 2 | 637 | 0.85 | 0.89 | 93 | empty |
| 3 | 553 | 0.84 | 0.90 | 79 | empty |
| 4 | 971 | 0.82 | 0.83 | 108 | empty |
| 5 | 138 | 0.78 | 0.96 | 21 | empty |
Interfaces
23 interfaces between chains.
- A–D · 2756 Ų buried · 41 hydrogen bonds · protein-protein
- C–D · 2734 Ų buried · 39 hydrogen bonds · protein-protein
- H–I · 2720 Ų buried · 39 hydrogen bonds · protein-protein
- E–F · 2715 Ų buried · 38 hydrogen bonds · protein-protein
- E–G · 2697 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- Q9WYB3 · AlphaFold monomer V2.0 prediction for L-arabinose isomerase (Q9WYB3) · a predicted model of the same protein · chain E 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 Q9WYB3
- Elsewhere: RCSB PDB 7CWV · PDBe 7CWV · UniProt Q9WYB3
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