Research workbench
Ribulose-1,5-bisphosphate carboxylase/oxygenase from Griffithsia monilis
Analyse Ribulose-1,5-bisphosphate carboxylase/oxygenase from Griffithsia monilis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8BDB
- Type
- protein
- Length
- 4,926 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.7
- Source
- Griffithsia monilis
- Molecule
- Ribulose bisphosphate carboxylase large chain; Ribulose bisphosphate carboxylase small…
- EC
- 4.1.1.39
- UniProt
- A7UM67, A7UM68
- Ligands
- BCT, CAP, MG
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · resolution 1.7 · 5 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) | protein | 480 | 42% helix, 16% strand | A7UM67 |
| B, D, F, H, J, L, N, P | Ribulose bisphosphate carboxylase small chain | protein | 138 | 22% helix, 30% strand | A7UM68 |
| C, G, K, O | Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) | protein | 479 | 43% helix, 16% strand | A7UM67 |
| E | Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) | protein | 468 | 43% helix, 16% strand | A7UM67 |
| I, M | Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) | protein | 479 | 42% helix, 16% strand | A7UM67 |
Ligands and binding sites
- BCT · Bicarbonate ion · ligand · 31 copies · chains A, B, C, D, E, F, G, H, I, K, L, M, N, O
- CAP · 2-carboxyarabinitol-1,5-diphosphate · sugar · 8 copies · chains A, C, E, G, I, K, M, O
- MG · Magnesium ion · metal · 8 copies · chains A, C, E, G, I, K, M, O
- EDO · 1,2-ethanediol · additive · 133 copies · chains A, O, P, C, B, D, M, N, E, I, J, F, K, L, G, 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 | 1149 | 0.81 | 0.83 | 115 | EDO |
| 2 | 886 | 0.81 | 0.83 | 71 | EDO |
| 3 | 456 | 0.76 | 0.85 | 61 | EDO |
| 4 | 446 | 0.75 | 0.84 | 58 | EDO |
| 5 | 548 | 0.74 | 0.82 | 76 | EDO |
Interfaces
40 interfaces between chains.
- K–L · 1569 Ų buried · 18 hydrogen bonds · protein-protein
- I–J · 1565 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1563 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1560 Ų buried · 19 hydrogen bonds · protein-protein
- E–F · 1559 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 modified (nonstandard, carboxylation).
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 A7UM67
- Every structure of UniProt A7UM68
- Elsewhere: RCSB PDB 8BDB · PDBe 8BDB · UniProt A7UM67 · UniProt A7UM68
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