Research workbench
Crystal structure of plastidial ribulose epimerase RPE1 from the model alga chlamydomonas reinhardtii
Analyse Crystal structure of plastidial ribulose epimerase RPE1 from the model alga… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7B1W
- Type
- protein
- Length
- 2,760 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribulose-phosphate 3-epimerase
- EC
- 5.1.3.1
- UniProt
- A8IKW6
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| J, B, C, E, L | Ribulose-phosphate 3-epimerase (EC 5.1.3.1) | protein | 229 | 39% helix, 21% strand | A8IKW6 |
| A, G, H, I, K | Ribulose-phosphate 3-epimerase (EC 5.1.3.1) | protein | 230 | 39% helix, 20% strand | A8IKW6 |
| D | Ribulose-phosphate 3-epimerase (EC 5.1.3.1) | protein | 231 | 37% helix, 20% strand | A8IKW6 |
| F | Ribulose-phosphate 3-epimerase (EC 5.1.3.1) | protein | 234 | 37% helix, 20% strand | A8IKW6 |
Ligands and binding sites
- ZN · Zinc ion · metal · 12 copies · chains J, A, B, C, D, E, F, G, H, I, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 272 | 0.83 | 0.95 | 42 | empty |
| 2 | 662 | 0.73 | 0.80 | 58 | empty |
| 3 | 659 | 0.71 | 0.78 | 62 | empty |
| 4 | 507 | 0.66 | 0.77 | 46 | empty |
| 5 | 459 | 0.62 | 0.76 | 55 | empty |
Interfaces
18 interfaces between chains.
- A–B · 1075 Ų buried · 12 hydrogen bonds · protein-protein
- J–E · 1060 Ų buried · 14 hydrogen bonds · protein-protein
- D–G · 1043 Ų buried · 12 hydrogen bonds · protein-protein
- I–L · 686 Ų buried · 9 hydrogen bonds · protein-protein
- C–K · 673 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 7B1W · Crystal structure of plastidial ribulose epimerase RPE1 from the model alga Chlamydomonas… · the same entry in another collection · chain J against J, 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 A8IKW6
- Elsewhere: RCSB PDB 7B1W · PDBe 7B1W · UniProt A8IKW6
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