Research workbench
Crystal structure of a putative mannose-6-phosphate isomerase (REUT_A1446) from ralstonia eutropha JMP134 at 2.10 a resolution
Analyse Crystal structure of a putative mannose-6-phosphate isomerase (REUT_A1446) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2OPK
- Type
- protein
- Length
- 440 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein
- UniProt
- Q471W7
- Ligands
- UNL, CL
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 0% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypothetical protein | protein | 110 | 0% helix, 51% strand | Q471W7 |
| B, D | Hypothetical protein | protein | 111 | 0% helix, 50% strand | Q471W7 |
| C | Hypothetical protein | protein | 108 | 0% helix, 51% strand | Q471W7 |
Ligands and binding sites
- UNL · Unknown ligand · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · chains C
- GOL · Glycerol · additive · 5 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 695 | 0.71 | 0.78 | 86 | GOL |
| 2 | 91 | 0.55 | 0.85 | 24 | UNL |
| 3 | 94 | 0.55 | 0.85 | 22 | UNL |
| 4 | 81 | 0.53 | 0.85 | 22 | UNL |
| 5 | 79 | 0.52 | 0.84 | 17 | UNL |
Interfaces
4 interfaces between chains.
- A–B · 1531 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1464 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 316 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 310 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 11 modified (engineered).
Compared structures
- 2OPK · Crystal structure of a putative mannose-6-phosphate isomerase (REUT_A1446) from ralstonia… · 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 Q471W7
- Elsewhere: RCSB PDB 2OPK · PDBe 2OPK · UniProt Q471W7
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