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Structure function studies of R. palustris rubisco (K192C mutant; cabp-bound)
Analyse Structure function studies of R. palustris rubisco (K192C mutant; cabp-bound) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KOZ
- Type
- protein
- Length
- 5,464 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribulose bisphosphate carboxylase
- EC
- 4.1.1.39
- UniProt
- Q6N0W9
- Ligands
- CAP, MG, CO3
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E, F, G, H, I, J, L | Ribulose bisphosphate carboxylase (EC 4.1.1.39) | protein | 455 | 44% helix, 18% strand | Q6N0W9 |
| C | Ribulose bisphosphate carboxylase (EC 4.1.1.39) | protein | 457 | 45% helix, 18% strand | Q6N0W9 |
| D, K | Ribulose bisphosphate carboxylase (EC 4.1.1.39) | protein | 456 | 45% helix, 18% strand | Q6N0W9 |
Ligands and binding sites
- CAP · 2-carboxyarabinitol-1,5-diphosphate · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- MG · Magnesium ion · metal · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- CO3 · Carbonate ion · ion · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
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 | 1053 | 0.84 | 0.85 | 118 | empty |
| 2 | 893 | 0.84 | 0.86 | 82 | empty |
| 3 | 1038 | 0.83 | 0.84 | 111 | empty |
| 4 | 929 | 0.83 | 0.85 | 97 | empty |
| 5 | 962 | 0.82 | 0.84 | 92 | empty |
Interfaces
27 interfaces between chains.
- E–F · 4257 Ų buried · 67 hydrogen bonds · protein-protein
- K–L · 4247 Ų buried · 65 hydrogen bonds · protein-protein
- A–B · 4225 Ų buried · 67 hydrogen bonds · protein-protein
- C–D · 4214 Ų buried · 67 hydrogen bonds · protein-protein
- G–H · 4211 Ų buried · 66 hydrogen bonds · protein-protein
Compared structures
- 5KOZ · Structure function studies of R. palustris RubisCO (K192C mutant; CABP-bound) · the same entry in another collection · chain L against L, 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 Q6N0W9
- Elsewhere: RCSB PDB 5KOZ · PDBe 5KOZ · UniProt Q6N0W9
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