MolNFT v1 · #127888 · protein
Rubisco from thalassiosira hyalina
5N9Z · Ribulose bisphosphate carboxylase large chain: “Rubisco from thalassiosira hyalina”. X-ray diffraction, 2 ligands (CAP, MG), 20 pockets (best druggability 0.88). MolNFT v1 #127888 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5N9Z
- Type
- protein
- Length
- 4,960 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribulose bisphosphate carboxylase large chain; Ribulose-1,5-bisphosphate…
- EC
- 4.1.1.39
- Ligands
- CAP, MG
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, H, F, D, B, C, E, G | Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) | protein | 481 | 42% helix, 16% strand | — |
| I, O, N, M, P, J, K, L | Ribulose-1,5-bisphosphate CARBOXYLASE/OXYGENASE small subunit | protein | 139 | 23% helix, 29% strand | — |
Ligands and binding sites
- CAP · 2-carboxyarabinitol-1,5-diphosphate · ligand · 8 copies · chains A, B, H, G, F, E, D, C
- MG · Magnesium ion · metal · 10 copies · chains A, B, I, J, H, G, F, E, D, C
- EDO · 1,2-ethanediol · additive · 19 copies · chains A, I, J, G, L, C, O, B, P, H, N, F, M, D, K, 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 394 | 0.88 | 0.96 | 75 | empty |
| 2 | 383 | 0.87 | 0.96 | 71 | empty |
| 3 | 374 | 0.87 | 0.96 | 72 | EDO |
| 4 | 280 | 0.85 | 0.96 | 53 | empty |
| 5 | 261 | 0.84 | 0.96 | 53 | empty |
Interfaces
56 interfaces between chains.
- A–B · 4916 Ų buried · 97 hydrogen bonds · protein-protein
- H–G · 4907 Ų buried · 95 hydrogen bonds · protein-protein
- D–C · 4893 Ų buried · 97 hydrogen bonds · protein-protein
- F–E · 4880 Ų buried · 91 hydrogen bonds · protein-protein
- E–K · 1610 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 64 modified (nonstandard, hydroxylation, carboxylation, methylation, oxidation).
Compared structures
- 5N9Z · Rubisco from Thalassiosira hyalina · 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 5N9Z · PDBe 5N9Z
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