Research workbench
Crystal structure of rubisco from chlamydomonas reinhardtii with a large-subunit V331A mutation
Analyse Crystal structure of rubisco from chlamydomonas reinhardtii with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2V63
- 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 0.81
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, F, G, H | Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) | protein | 466 | 44% helix, 17% strand | P00877 |
| D, E | Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) | protein | 464 | 44% 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 | 28% 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 · 46 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
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 | 143 | 0.81 | 0.98 | 48 | CAP |
| 2 | 145 | 0.80 | 0.97 | 45 | CAP |
| 3 | 142 | 0.80 | 0.97 | 44 | CAP, EDO |
| 4 | 139 | 0.80 | 0.97 | 43 | CAP, EDO |
| 5 | 145 | 0.80 | 0.97 | 44 | CAP, EDO |
Interfaces
48 interfaces between chains.
- G–H · 4827 Ų buried · 90 hydrogen bonds · protein-protein
- A–B · 4821 Ų buried · 90 hydrogen bonds · protein-protein
- E–F · 4820 Ų buried · 89 hydrogen bonds · protein-protein
- C–D · 4797 Ų buried · 91 hydrogen bonds · protein-protein
- C–K · 2021 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 modified, 4 disulfide (hydroxylation, methylation, carboxylation, nonstandard, disulfide).
Compared structures
- 2V63 · Crystal structure of Rubisco from Chlamydomonas reinhardtii with a large-subunit V331A… · 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 2V63 · PDBe 2V63 · UniProt P00877 · UniProt P00873
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