Research workbench
Crystal Structure of Ribose-5-phosphate Isomerase from Brucella melitensis 16M
Analyse Crystal Structure of Ribose-5-phosphate Isomerase from Brucella melitensis 16M in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JLA
- Type
- protein
- Length
- 1,032 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.45
- Source
- Burkholderia xenovorans (strain LB400)
- Molecule
- Putative short-chain dehydrogenase/reductase
- UniProt
- Q13GR0
- Ligands
- NAD
- Pockets
- 14 · best druggability 0.83
Structure
x-ray diffraction · resolution 1.45 · 3 distinct chains · 50% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative short-chain dehydrogenase/reductase | protein | 257 | 50% helix, 17% strand | Q13GR0 |
| B, C | Putative short-chain dehydrogenase/reductase | protein | 258 | 50% helix, 17% strand | Q13GR0 |
| D | Putative short-chain dehydrogenase/reductase | protein | 259 | 50% helix, 17% strand | Q13GR0 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1190 | 0.83 | 0.84 | 65 | empty |
| 2 | 427 | 0.77 | 0.86 | 48 | NAD |
| 3 | 416 | 0.76 | 0.85 | 48 | NAD |
| 4 | 416 | 0.76 | 0.85 | 48 | NAD |
| 5 | 395 | 0.75 | 0.85 | 44 | NAD |
Interfaces
6 interfaces between chains.
- A–B · 1614 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1607 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 1373 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 1361 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 1057 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5JLA · Crystal structure of ribose-5-phosphate isomerase from brucella melitensis 16M · 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 Q13GR0
- Elsewhere: RCSB PDB 5JLA · PDBe 5JLA · UniProt Q13GR0
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