MolNFT v1 · #51394 · protein
Crystal structure of chlamydomonas reinhardtii rubisco with a large- subunit mutation D473E
2V69 · Ribulose bisphosphate carboxylase large chain: “Crystal structure of chlamydomonas reinhardtii rubisco with a large- subunit mutation D473E”. X-ray diffraction, 2 ligands (CAP, MG), 20 pockets (best druggability 0.78). MolNFT v1…
- PDB
- 2V69
- Type
- protein
- Length
- 4,801 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 0.78
Structure
x-ray diffraction · 7 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) | protein | 459 | 44% helix, 17% strand | P00877 |
| B | Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) | protein | 460 | 43% helix, 17% strand | P00877 |
| C | Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) | protein | 459 | 44% helix, 17% strand | P00877 |
| D | Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) | protein | 464 | 43% helix, 17% strand | P00877 |
| F, G | Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) | protein | 461 | 43% helix, 17% strand | P00877 |
| H | Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) | protein | 458 | 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 | 23% 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 · 24 copies · chains A, B, C, D, E, F, G, M, H
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 | 896 | 0.78 | 0.81 | 64 | empty |
| 2 | 907 | 0.78 | 0.81 | 61 | empty |
| 3 | 919 | 0.78 | 0.80 | 61 | empty |
| 4 | 897 | 0.77 | 0.81 | 64 | empty |
| 5 | 98 | 0.77 | 0.98 | 26 | empty |
Interfaces
50 interfaces between chains.
- C–D · 4789 Ų buried · 87 hydrogen bonds · protein-protein
- G–H · 4697 Ų buried · 82 hydrogen bonds · protein-protein
- E–F · 4690 Ų buried · 87 hydrogen bonds · protein-protein
- A–B · 4668 Ų buried · 80 hydrogen bonds · protein-protein
- C–K · 2044 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 modified, 4 disulfide (hydroxylation, methylation, carboxylation, nonstandard, disulfide).
Compared structures
- 2V69 · Crystal structure of Chlamydomonas reinhardtii Rubisco with a large- subunit mutation… · 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 2V69 · PDBe 2V69 · UniProt P00877 · UniProt P00873
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