Research workbench
Structure of rice rubisco in complex with 6PG
Analyse Structure of rice rubisco in complex with 6PG in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3AXM
- Type
- protein
- Length
- 4,520 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
- P0C512, Q0INY7
- Ligands
- 6PG, MG, NME
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 6 distinct chains · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) | protein | 444 | 45% helix, 18% strand | P0C512 |
| S, T, U, V, W, X, Y, Z | Ribulose bisphosphate carboxylase small chain, chloroplastic (EC 4.1.1.39) | protein | 122 | 22% helix, 24% strand | Q0INY7 |
| B | Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) | protein | 443 | 45% helix, 18% strand | P0C512 |
| C | Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) | protein | 443 | 45% helix, 18% strand | P0C512 |
| D, F, H | Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) | protein | 444 | 44% helix, 18% strand | P0C512 |
| E, G | Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) | protein | 441 | 46% helix, 18% strand | P0C512 |
Ligands and binding sites
- 6PG · 6-phosphogluconic acid · 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
- NME · Methylamine · ion · 8 copies · chains A, S, B, T, C, U, D, V, E, W, F, X, G, Y, H, Z
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 | 1011 | 0.84 | 0.85 | 139 | empty |
| 2 | 1175 | 0.82 | 0.83 | 119 | empty |
| 3 | 1168 | 0.80 | 0.82 | 106 | empty |
| 4 | 979 | 0.79 | 0.80 | 72 | empty |
| 5 | 73 | 0.77 | 0.99 | 22 | empty |
Interfaces
48 interfaces between chains.
- C–D · 3869 Ų buried · 66 hydrogen bonds · protein-protein
- E–F · 3868 Ų buried · 68 hydrogen bonds · protein-protein
- A–B · 3859 Ų buried · 61 hydrogen bonds · protein-protein
- G–H · 3825 Ų buried · 64 hydrogen bonds · protein-protein
- G–Y · 1898 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (carboxylation).
Compared structures
- 3AXM · Structure of rice Rubisco in complex with 6PG · the same entry in another collection · chain Z against Z, 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 P0C512
- Every structure of UniProt Q0INY7
- Elsewhere: RCSB PDB 3AXM · PDBe 3AXM · UniProt P0C512 · UniProt Q0INY7
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.