Research workbench
Crystal structure of pseudomonas stutzeri L-rhamnose isomerase mutant D327N in complex with D-psicose
Analyse Crystal structure of pseudomonas stutzeri L-rhamnose isomerase mutant D327N in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ITO
- Type
- protein
- Length
- 1,689 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-rhamnose isomerase
- EC
- 5.3.1.14
- UniProt
- Q75WH8
- Ligands
- PSV, MN
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 50% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | L-rhamnose isomerase (EC 5.3.1.14) | protein | 421 | 50% helix, 10% strand | Q75WH8 |
| C | L-rhamnose isomerase (EC 5.3.1.14) | protein | 428 | 49% helix, 11% strand | Q75WH8 |
| D | L-rhamnose isomerase (EC 5.3.1.14) | protein | 419 | 51% helix, 11% strand | Q75WH8 |
Ligands and binding sites
- PSV · alpha-D-psicofuranose · ligand · 4 copies · chains A, B, C, D
- MN · Manganese (II) ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 996 | 0.83 | 0.84 | 100 | empty |
| 2 | 1024 | 0.82 | 0.84 | 100 | empty |
| 3 | 141 | 0.81 | 0.98 | 33 | empty |
| 4 | 196 | 0.81 | 0.95 | 44 | empty |
| 5 | 189 | 0.80 | 0.95 | 39 | empty |
Interfaces
6 interfaces between chains.
- B–D · 2468 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 2439 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 2227 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1971 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 1725 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 3ITO · Crystal structure of Pseudomonas stutzeri L-rhamnose isomerase mutant D327N in complex… · the same entry in another collection · chain A against A, TM-score 1.00
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 Q75WH8
- Elsewhere: RCSB PDB 3ITO · PDBe 3ITO · UniProt Q75WH8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.