Research workbench
Crystal structure of activated ribulose-1,5-bisphosphate CARBOXYLASE/OXYGENASE (rubisco) from green alga, chlamydomonas reinhardtii complexed with 2-carboxyarabinitol-1,5-bisphosphate (2- cabp)
Analyse Crystal structure of activated ribulose-1,5-bisphosphate CARBOXYLASE/OXYGENASE… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1IR2
- Type
- protein
- Length
- 9,704 residues
- Chains
- 32
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Large subunit of rubisco; Small subunit of rubisco
- EC
- 4.1.1.39
- UniProt
- P00877, P08475
- Ligands
- CAP, MG
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 6 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, H | Large subunit of rubisco (EC 4.1.1.39) | protein | 468 | 43% helix, 17% strand | P00877 |
| I, J, K, L, M, N, O, P, 1, 2, 3, 4, 5, 6, 7, 8 | Small subunit of rubisco (EC 4.1.1.39) | protein | 140 | 27% helix, 21% strand | P08475 |
| B, D | Large subunit of rubisco (EC 4.1.1.39) | protein | 467 | 43% helix, 17% strand | P00877 |
| C, G, T, W, X, Z | Large subunit of rubisco (EC 4.1.1.39) | protein | 466 | 44% helix, 17% strand | P00877 |
| E, F, S, Y | Large subunit of rubisco (EC 4.1.1.39) | protein | 465 | 44% helix, 17% strand | P00877 |
| U, V | Large subunit of rubisco (EC 4.1.1.39) | protein | 469 | 43% helix, 17% strand | P00877 |
Ligands and binding sites
- CAP · 2-carboxyarabinitol-1,5-diphosphate · ligand · 16 copies · chains A, E, B, F, C, G, D, H, S, W, T, X, U, Y, V, Z
- MG · Magnesium ion · metal · 16 copies · chains A, E, B, F, C, G, D, H, S, W, T, X, U, Y, V, Z
- GOL · Glycerol · additive · 40 copies · chains A, B, F, C, D, E, H, G, S, W, T, U, V, Z, X, Y
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 | 140 | 0.81 | 0.98 | 44 | CAP |
| 2 | 145 | 0.80 | 0.98 | 45 | MG, CAP |
| 3 | 130 | 0.80 | 0.98 | 44 | MG, CAP |
| 4 | 862 | 0.79 | 0.82 | 65 | GOL |
| 5 | 899 | 0.79 | 0.81 | 63 | GOL |
Interfaces
99 interfaces between chains.
- D–H · 4805 Ų buried · 93 hydrogen bonds · protein-protein
- C–G · 4804 Ų buried · 91 hydrogen bonds · protein-protein
- T–X · 4801 Ų buried · 91 hydrogen bonds · protein-protein
- U–Y · 4799 Ų buried · 91 hydrogen bonds · protein-protein
- A–E · 4799 Ų buried · 92 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 96 modified (hydroxylation, methylation, carboxylation, nonstandard).
Compared structures
- 1IR2 · Crystal Structure of Activated Ribulose-1,5-bisphosphate Carboxylase/oxygenase (Rubisco)… · the same entry in another collection · chain F against F, 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 P00877
- Every structure of UniProt P08475
- Elsewhere: RCSB PDB 1IR2 · PDBe 1IR2 · UniProt P00877 · UniProt P08475
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.