MolNFT v1 · #114860 · protein
GWS1B rubisco: form II rubisco derived from uncultivated gallionellacea species (unliganded form)
5C2C: “GWS1B rubisco: form II rubisco derived from uncultivated gallionellacea species (unliganded form)”. X-ray diffraction, 2 ligands (MG, CL), 14 pockets (best druggability 0.80). MolNFT v1 #114860 on GenesisL1: 3D structure, binding…
- PDB
- 5C2C
- Type
- protein
- Length
- 1,330 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Form II rubisco
- Ligands
- MG, CL
- Pockets
- 14 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Form II rubisco | protein | 448 | 45% helix, 17% strand | — |
| B | Form II rubisco | protein | 435 | 45% helix, 18% strand | — |
| C | Form II rubisco | protein | 447 | 45% helix, 17% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 126 | 0.80 | 0.98 | 32 | empty |
| 2 | 839 | 0.78 | 0.81 | 94 | empty |
| 3 | 501 | 0.71 | 0.81 | 60 | CL, MG |
| 4 | 498 | 0.71 | 0.81 | 65 | MG |
| 5 | 400 | 0.65 | 0.79 | 35 | empty |
Interfaces
3 interfaces between chains.
- B–C · 3157 Ų buried · 44 hydrogen bonds · protein-protein
- A–B · 1121 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 75 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 3 modified (carboxylation).
Compared structures
- 5C2C · 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 5C2C · PDBe 5C2C
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