Research workbench
Crystal structure of rubisco from promineofilum breve
Analyse Crystal structure of rubisco from promineofilum breve in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6URA
- Type
- protein
- Length
- 1,762 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribulose bisphosphate carboxylase large chain
- EC
- 4.1.1.39
- UniProt
- A0A160T9D2
- Ligands
- CAP, MG
- Pockets
- 19 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) | protein | 441 | 44% helix, 18% strand | A0A160T9D2 |
| B, D | Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) | protein | 440 | 44% helix, 18% strand | A0A160T9D2 |
Ligands and binding sites
- CAP · 2-carboxyarabinitol-1,5-diphosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 576 | 0.80 | 0.86 | 122 | CAP, MG |
| 2 | 143 | 0.78 | 0.96 | 46 | CAP |
| 3 | 168 | 0.77 | 0.94 | 49 | CAP |
| 4 | 100 | 0.76 | 0.97 | 37 | CAP, MG |
| 5 | 61 | 0.59 | 0.91 | 21 | empty |
Interfaces
6 interfaces between chains.
- C–D · 4446 Ų buried · 94 hydrogen bonds · protein-protein
- A–B · 4414 Ų buried · 89 hydrogen bonds · protein-protein
- A–D · 377 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 325 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 44 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 modified (carboxylation).
Compared structures
- 6URA · Crystal structure of RUBISCO from Promineofilum breve · 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 A0A160T9D2
- Elsewhere: RCSB PDB 6URA · PDBe 6URA · UniProt A0A160T9D2
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