Research workbench
Rubisco from chlamydomonas reinhardtii
Analyse Rubisco from chlamydomonas reinhardtii in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1GK8
- Type
- protein
- Length
- 2,374 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribulose-1,5 bisphosphate carboxylase large chain; Ribulose bisphosphate carboxylase…
- EC
- 4.1.1.39
- UniProt
- P00877, P00873
- Ligands
- CAP, MG
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Ribulose-1,5 bisphosphate carboxylase large chain (EC 4.1.1.39) | protein | 469 | 44% helix, 16% strand | P00877 |
| E | Ribulose-1,5 bisphosphate carboxylase large chain (EC 4.1.1.39) | protein | 465 | 44% helix, 17% strand | P00877 |
| G | Ribulose-1,5 bisphosphate carboxylase large chain (EC 4.1.1.39) | protein | 467 | 44% helix, 16% strand | P00877 |
| I, K, M, O | Ribulose bisphosphate carboxylase small chain 1 (EC 4.1.1.39) | protein | 126 | 28% helix, 23% strand | P00873 |
Ligands and binding sites
- CAP · 2-carboxyarabinitol-1,5-diphosphate · ligand · 4 copies · chains A, C, E, G
- MG · Magnesium ion · metal · 4 copies · chains A, C, E, G
- EDO · 1,2-ethanediol · additive · 33 copies · chains A, C, E, G, I, K, M, O
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 106 | 0.77 | 0.97 | 28 | empty |
| 2 | 106 | 0.76 | 0.97 | 29 | empty |
| 3 | 100 | 0.76 | 0.96 | 24 | empty |
| 4 | 103 | 0.76 | 0.96 | 24 | empty |
| 5 | 355 | 0.63 | 0.79 | 49 | empty |
Interfaces
16 interfaces between chains.
- A–I · 1997 Ų buried · 22 hydrogen bonds · protein-protein
- C–K · 1995 Ų buried · 24 hydrogen bonds · protein-protein
- E–M · 1994 Ų buried · 23 hydrogen bonds · protein-protein
- G–O · 1992 Ų buried · 21 hydrogen bonds · protein-protein
- G–M · 1089 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified, 3 disulfide (hydroxylation, methylation, carboxylation, nonstandard, disulfide).
Compared structures
- 1GK8 · Rubisco from Chlamydomonas reinhardtii · the same entry in another collection · chain O against O, TM-score 1.00
- P00877 · AlphaFold monomer V2.0 prediction for ribulose bisphosphate carboxylase large chain… · a predicted model of the same protein · chain E against A, TM-score 1.00
- P00873 · AlphaFold monomer V2.0 prediction for ribulose bisphosphate carboxylase small subunit… · a predicted model of the same protein · chain I 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 P00877
- Every structure of UniProt P00873
- Elsewhere: RCSB PDB 1GK8 · PDBe 1GK8 · UniProt P00877 · UniProt P00873
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