Research workbench
Crystal structure of chlamydomonas reinhardtii rubisco with a large- subunit C192S mutation
Analyse Crystal structure of chlamydomonas reinhardtii rubisco with a large- subunit… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VDI
- Type
- protein
- Length
- 4,844 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribulose bisphosphate carboxylase large chain; Ribulose bisphosphate carboxylase small…
- EC
- 4.1.1.39
- UniProt
- P00877, P00873
- Ligands
- CAP, MG
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, E, F, H | Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) | protein | 465 | 44% helix, 17% strand | P00877 |
| B | Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) | protein | 468 | 44% helix, 17% strand | P00877 |
| G | Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) | protein | 466 | 43% helix, 17% strand | P00877 |
| I, J, K, L, M, N, O, P | Ribulose bisphosphate carboxylase small chain 1 (EC 4.1.1.39) | protein | 140 | 27% helix, 22% strand | P00873 |
Ligands and binding sites
- CAP · 2-carboxyarabinitol-1,5-diphosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- EDO · 1,2-ethanediol · additive · 43 copies · chains A, B, C, D, E, F, G, H, J, K, L, N, 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 165 | 0.82 | 0.98 | 46 | MG, CAP, EDO |
| 2 | 146 | 0.81 | 0.98 | 45 | CAP |
| 3 | 145 | 0.81 | 0.98 | 46 | CAP, EDO |
| 4 | 149 | 0.81 | 0.97 | 47 | CAP, EDO |
| 5 | 1120 | 0.80 | 0.82 | 147 | empty |
Interfaces
48 interfaces between chains.
- A–B · 4833 Ų buried · 88 hydrogen bonds · protein-protein
- C–D · 4823 Ų buried · 89 hydrogen bonds · protein-protein
- G–H · 4821 Ų buried · 89 hydrogen bonds · protein-protein
- E–F · 4816 Ų buried · 88 hydrogen bonds · protein-protein
- H–P · 2025 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 modified, 4 disulfide (hydroxylation, methylation, carboxylation, nonstandard, disulfide).
Compared structures
- 2VDI · Crystal structure of Chlamydomonas reinhardtii Rubisco with a large- subunit C192S… · the same entry in another collection · chain P against P, 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 P00873
- Elsewhere: RCSB PDB 2VDI · PDBe 2VDI · UniProt P00877 · UniProt P00873
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.