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Crystal structure of ribose-1,5-bisphosphate isomerase mutant C135S from pyrococcus horikoshii OT3 in complex with ribose-1,5- bisphosphate
Analyse Crystal structure of ribose-1,5-bisphosphate isomerase mutant C135S from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YFS
- Type
- protein
- Length
- 966 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribose 1,5-bisphosphate isomerase
- EC
- 5.3.1.29
- UniProt
- O57947
- Ligands
- RI2, K, CL
- Pockets
- 12 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Ribose 1,5-bisphosphate isomerase (EC 5.3.1.29) | protein | 322 | 52% helix, 13% strand | O57947 |
Ligands and binding sites
- RI2 · 1,5-di-O-phosphono-alpha-D-ribofuranose · ligand · 3 copies · chains A, B, C
- K · Potassium ion · metal · 3 copies · chains A, B, C
- CL · Chloride ion · ion · 3 copies · chains A, B, C
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 909 | 0.79 | 0.81 | 97 | CL |
| 2 | 80 | 0.67 | 0.93 | 25 | RI2 |
| 3 | 73 | 0.66 | 0.93 | 26 | RI2 |
| 4 | 83 | 0.64 | 0.91 | 27 | RI2 |
| 5 | 268 | 0.59 | 0.79 | 42 | empty |
Interfaces
3 interfaces between chains.
- A–C · 731 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 718 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 718 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5YFS · Crystal structure of ribose-1,5-bisphosphate isomerase mutant C135S from Pyrococcus… · the same entry in another collection · chain A against A, TM-score 1.00
- O57947 · AlphaFold monomer V2.0 prediction for ribose 1,5-bisphosphate isomerase (O57947) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 O57947
- Elsewhere: RCSB PDB 5YFS · PDBe 5YFS · UniProt O57947
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