MolNFT v1 · #114864 · protein
GWS1B rubisco: form II rubisco derived from uncultivated gallionellacea species (cabp-bound).
5C2G: “GWS1B rubisco: form II rubisco derived from uncultivated gallionellacea species (cabp-bound).”. X-ray diffraction, 2 ligands (CAP, MG), 20 pockets (best druggability 0.81). MolNFT v1 #114864 on GenesisL1: 3D structure, binding sites…
- PDB
- 5C2G
- Type
- protein
- Length
- 2,749 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Form II rubisco
- Ligands
- CAP, MG
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 5 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Form II rubisco | protein | 461 | 43% helix, 17% strand | — |
| B | Form II rubisco | protein | 454 | 44% helix, 18% strand | — |
| C | Form II rubisco | protein | 459 | 43% helix, 17% strand | — |
| E | Form II rubisco | protein | 457 | 43% helix, 18% strand | — |
| F | Form II rubisco | protein | 457 | 44% helix, 18% strand | — |
Ligands and binding sites
- CAP · 2-carboxyarabinitol-1,5-diphosphate · ligand · 6 copies · chains A, C, B, F, D, E
- MG · Magnesium ion · metal · 6 copies · chains A, C, B, F, 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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 125 | 0.81 | 0.98 | 31 | empty |
| 2 | 122 | 0.81 | 0.98 | 31 | empty |
| 3 | 119 | 0.80 | 0.98 | 30 | empty |
| 4 | 682 | 0.79 | 0.84 | 91 | empty |
| 5 | 1188 | 0.78 | 0.80 | 106 | empty |
Interfaces
12 interfaces between chains.
- A–C · 4430 Ų buried · 73 hydrogen bonds · protein-protein
- D–E · 4422 Ų buried · 70 hydrogen bonds · protein-protein
- B–F · 4180 Ų buried · 63 hydrogen bonds · protein-protein
- C–D · 1101 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 1096 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (carboxylation).
Compared structures
- 5C2G · GWS1B RubisCO: Form II RubisCO derived from uncultivated Gallionellacea species… · 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
- Elsewhere: RCSB PDB 5C2G · PDBe 5C2G
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