MolNFT v1 · #173503 · protein
Crystal structure of plastidial ribulose epimerase RPE1 from the model alga chlamydomonas reinhardtii
7B1W · Ribulose-phosphate 3-epimerase: “Crystal structure of plastidial ribulose epimerase RPE1 from the model alga chlamydomonas reinhardtii”. X-ray diffraction, 1 ligand (ZN), 20 pockets (best druggability 0.83). MolNFT v1 #173503 on…
- 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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