Research workbench
Crystal structure of decameric methanococcoides burtonii rubisco complexed with 2-carboxyarabinitol bisphosphate
Analyse Crystal structure of decameric methanococcoides burtonii rubisco complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MAC
- Type
- protein
- Length
- 2,363 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribulose-1,5-bisphosphate carboxylase-oxygenase type III
- EC
- 4.1.1.39
- UniProt
- Q12TQ0
- Ligands
- CAP, MG, CL
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Ribulose-1,5-bisphosphate carboxylase-oxygenase type III (EC 4.1.1.39) | protein | 473 | 43% helix, 16% strand | Q12TQ0 |
| C | Ribulose-1,5-bisphosphate carboxylase-oxygenase type III (EC 4.1.1.39) | protein | 472 | 40% helix, 17% strand | Q12TQ0 |
| E | Ribulose-1,5-bisphosphate carboxylase-oxygenase type III (EC 4.1.1.39) | protein | 472 | 41% helix, 16% strand | Q12TQ0 |
Ligands and binding sites
- CAP · 2-carboxyarabinitol-1,5-diphosphate · ligand · 5 copies · chains A, B, C, D, E
- MG · Magnesium ion · metal · 10 copies · chains A, B, D, C, E
- CL · Chloride ion · ion · 5 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 90 | 0.75 | 0.98 | 31 | CAP, MG |
| 2 | 86 | 0.75 | 0.98 | 31 | CAP, MG |
| 3 | 86 | 0.74 | 0.97 | 30 | CAP |
| 4 | 210 | 0.72 | 0.89 | 56 | CAP |
| 5 | 352 | 0.64 | 0.79 | 43 | empty |
Interfaces
8 interfaces between chains.
- C–D · 4187 Ų buried · 90 hydrogen bonds · protein-protein
- A–B · 4167 Ų buried · 96 hydrogen bonds · protein-protein
- B–D · 758 Ų buried · 20 hydrogen bonds · protein-protein
- C–E · 755 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 754 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 modified (carboxylation).
Compared structures
- 5MAC · Crystal structure of decameric Methanococcoides burtonii Rubisco complexed with… · the same entry in another collection · chain A against A, 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 Q12TQ0
- Elsewhere: RCSB PDB 5MAC · PDBe 5MAC · UniProt Q12TQ0
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