Research workbench
Crystal structure of ribose-5-phosphate isomerase a from pseudomonas aeruginosa
Analyse Crystal structure of ribose-5-phosphate isomerase a from pseudomonas aeruginosa in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4X84
- Type
- protein
- Length
- 899 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribose-5-phosphate isomerase a
- EC
- 5.3.1.6
- UniProt
- Q9I6G1
- Pockets
- 7 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Ribose-5-phosphate isomerase a (EC 5.3.1.6) | protein | 224 | 36% helix, 28% strand | Q9I6G1 |
| B | Ribose-5-phosphate isomerase a (EC 5.3.1.6) | protein | 229 | 36% helix, 28% strand | Q9I6G1 |
| D | Ribose-5-phosphate isomerase a (EC 5.3.1.6) | protein | 222 | 36% helix, 28% strand | Q9I6G1 |
Ligands and binding sites
- FLC · Citrate anion · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1049 | 0.72 | 0.76 | 136 | empty |
| 2 | 269 | 0.60 | 0.79 | 50 | empty |
| 3 | 117 | 0.42 | 0.76 | 25 | empty |
| 4 | 61 | 0.40 | 0.81 | 16 | FLC |
| 5 | 64 | 0.40 | 0.81 | 18 | FLC |
Interfaces
5 interfaces between chains.
- A–D · 1195 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1177 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 351 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 235 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 74 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4X84 · Crystal structure of Ribose-5-phosphate isomerase A from Pseudomonas aeruginosa · the same entry in another collection · chain A against A, TM-score 1.00
- Q9I6G1 · AlphaFold monomer V2.0 prediction for ribose-5-phosphate isomerase a (Q9I6G1) · a predicted model of the same protein · chain D against A, TM-score 0.99
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 Q9I6G1
- Elsewhere: RCSB PDB 4X84 · PDBe 4X84 · UniProt Q9I6G1
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