MolNFT v1 · #51642 · protein
Crystal structure of chlamydomonas reinhardtii rubisco with a large-subunit C172S mutation
2VDH · Ribulose bisphosphate carboxylase large chain: “Crystal structure of chlamydomonas reinhardtii rubisco with a large-subunit C172S mutation”. X-ray diffraction, 2 ligands (CAP, MG), 20 pockets (best druggability 0.82). MolNFT v1…
- PDB
- 2VDH
- Type
- protein
- Length
- 4,849 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, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, E, 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 |
| C, F, G | Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) | protein | 467 | 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 | 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 · 57 copies · chains A, B, C, D, E, F, P, G, H, I, J, K, L, M, 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 | 1105 | 0.82 | 0.83 | 101 | empty |
| 2 | 1122 | 0.82 | 0.83 | 107 | empty |
| 3 | 143 | 0.81 | 0.98 | 49 | CAP, EDO |
| 4 | 142 | 0.81 | 0.98 | 44 | MG, CAP, EDO |
| 5 | 137 | 0.80 | 0.98 | 43 | CAP, EDO |
Interfaces
48 interfaces between chains.
- G–H · 4835 Ų buried · 92 hydrogen bonds · protein-protein
- E–F · 4831 Ų buried · 90 hydrogen bonds · protein-protein
- A–B · 4828 Ų buried · 92 hydrogen bonds · protein-protein
- C–D · 4822 Ų buried · 91 hydrogen bonds · protein-protein
- A–I · 2008 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 modified, 12 disulfide (hydroxylation, methylation, disulfide, carboxylation, nonstandard).
Compared structures
- 2VDH · Crystal structure of Chlamydomonas reinhardtii Rubisco with a large- subunit C172S… · 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 2VDH · PDBe 2VDH · UniProt P00877 · UniProt P00873
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