Research workbench
Crystal structure of a putative ribose 5-phosphate isomerase (SARO_3514) from novosphingobium aromaticivorans dsm at 1.81 a resolution
Analyse Crystal structure of a putative ribose 5-phosphate isomerase (SARO_3514) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3C5Y
- Type
- protein
- Length
- 3,394 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RIBOSE/GALACTOSE isomerase
- UniProt
- A4XEL3
- Ligands
- NO3
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 6 distinct chains · 54% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G, O, P | RIBOSE/GALACTOSE isomerase | protein | 211 | 55% helix, 11% strand | A4XEL3 |
| B, C, I, J, K, M, N | RIBOSE/GALACTOSE isomerase | protein | 212 | 54% helix, 11% strand | A4XEL3 |
| E | RIBOSE/GALACTOSE isomerase | protein | 215 | 53% helix, 11% strand | A4XEL3 |
| F | RIBOSE/GALACTOSE isomerase | protein | 213 | 54% helix, 11% strand | A4XEL3 |
| H | RIBOSE/GALACTOSE isomerase | protein | 214 | 53% helix, 11% strand | A4XEL3 |
| L | RIBOSE/GALACTOSE isomerase | protein | 213 | 54% helix, 11% strand | A4XEL3 |
Ligands and binding sites
- NO3 · Nitrate ion · ion · 8 copies · chains F, G, J, I, O, P
- EDO · 1,2-ethanediol · additive · 61 copies · chains A, B, H, C, D, G, J, E, F, I, L, K, O, M, N, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 913 | 0.87 | 0.88 | 90 | EDO |
| 2 | 954 | 0.87 | 0.88 | 96 | EDO |
| 3 | 940 | 0.87 | 0.88 | 91 | EDO |
| 4 | 913 | 0.86 | 0.88 | 93 | EDO |
| 5 | 779 | 0.68 | 0.75 | 76 | NO3, EDO |
Interfaces
35 interfaces between chains.
- G–H · 1989 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 1986 Ų buried · 15 hydrogen bonds · protein-protein
- K–L · 1976 Ų buried · 17 hydrogen bonds · protein-protein
- M–N · 1964 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1963 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 160 modified (engineered, oxidation).
Compared structures
- 3C5Y · Crystal structure of a putative ribose 5-phosphate isomerase (saro_3514) from… · 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 A4XEL3
- Elsewhere: RCSB PDB 3C5Y · PDBe 3C5Y · UniProt A4XEL3
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