Research workbench
Crystal structure of ribose-1,5-bisphosphate isomerase mutant D204N from pyrococcus horikoshii OT3 in complex with ribose-1,5- bisphosphate and gmp
Analyse Crystal structure of ribose-1,5-bisphosphate isomerase mutant D204N from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YG7
- 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
- G, RI2, K
- Pockets
- 13 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 53% 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 | 53% helix, 13% strand | O57947 |
Ligands and binding sites
- G · Guanosine-5'-monophosphate · ligand · 5 copies · chains A, C, B
- 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
- MRD · (4R)-2-methylpentane-2,4-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 660 | 0.75 | 0.81 | 75 | G |
| 2 | 93 | 0.65 | 0.91 | 28 | RI2 |
| 3 | 94 | 0.65 | 0.91 | 28 | RI2 |
| 4 | 89 | 0.64 | 0.91 | 28 | RI2 |
| 5 | 202 | 0.60 | 0.81 | 24 | G |
Interfaces
3 interfaces between chains.
- A–C · 750 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 730 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 717 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5YG7 · Crystal structure of ribose-1,5-bisphosphate isomerase mutant D204N 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 5YG7 · PDBe 5YG7 · UniProt O57947
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