MolNFT v1 · #100883 · protein
The crystal structure of a rubisco-like protein (mtnw) from alicyclobacillus acidocaldarius subsp. acidocaldarius dsm 446
4NAS · Ribulose-bisphosphate carboxylase: “The crystal structure of a rubisco-like protein (mtnw) from alicyclobacillus acidocaldarius subsp.…”. X-ray diffraction, 2 ligands (CA, CL), 20 pockets (best druggability 0.79). MolNFT v1 #100883…
- PDB
- 4NAS
- Type
- protein
- Length
- 1,584 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribulose-bisphosphate carboxylase
- EC
- 4.1.1.39
- UniProt
- C8WQ56
- Ligands
- CA, CL
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribulose-bisphosphate carboxylase (EC 4.1.1.39) | protein | 397 | 47% helix, 19% strand | C8WQ56 |
| B | Ribulose-bisphosphate carboxylase (EC 4.1.1.39) | protein | 399 | 45% helix, 19% strand | C8WQ56 |
| C | Ribulose-bisphosphate carboxylase (EC 4.1.1.39) | protein | 396 | 45% helix, 19% strand | C8WQ56 |
| D | Ribulose-bisphosphate carboxylase (EC 4.1.1.39) | protein | 392 | 45% helix, 19% strand | C8WQ56 |
Ligands and binding sites
- CA · Calcium ion · metal · 7 copies · chains A, B, C, D
- CL · Chloride ion · ion · chains A, B
- FMT · Formic acid · additive · 3 copies · chains A, B
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 106 | 0.79 | 0.98 | 24 | empty |
| 2 | 113 | 0.79 | 0.97 | 24 | GOL |
| 3 | 907 | 0.75 | 0.78 | 73 | FMT, CA |
| 4 | 529 | 0.68 | 0.78 | 38 | CA |
| 5 | 627 | 0.67 | 0.77 | 57 | CA |
Interfaces
5 interfaces between chains.
- A–B · 2758 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 2658 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 212 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 103 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 51 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 modified (engineered, carboxylation).
Compared structures
- 4NAS · The crystal structure of a rubisco-like protein (MtnW) from Alicyclobacillus… · 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 C8WQ56
- Elsewhere: RCSB PDB 4NAS · PDBe 4NAS · UniProt C8WQ56
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