Research workbench
Structure of rubisco from rhodobacter sphaeroides in complex with cabp
Analyse Structure of rubisco from rhodobacter sphaeroides in complex with cabp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NV3
- Type
- protein
- Length
- 4,768 residues
- Chains
- 16
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribulose bisphosphate carboxylase large chain; Ribulose bisphosphate carboxylase small…
- EC
- 4.1.1.39
- UniProt
- P27997, P27998
- Ligands
- CAP, MG
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 2 distinct chains · 35% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) | protein | 467 | 39% helix, 18% strand | P27997 |
| I, J, K, L, M, N, O, P | Ribulose bisphosphate carboxylase small chain 1 (EC 4.1.1.39) | protein | 129 | 22% helix, 30% strand | P27998 |
Ligands and binding sites
- CAP · 2-carboxyarabinitol-1,5-diphosphate · ligand · 8 copies · chains A, E, B, F, C, G, D, H
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
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 | 159 | 0.83 | 0.98 | 26 | empty |
| 2 | 811 | 0.83 | 0.86 | 61 | empty |
| 3 | 160 | 0.82 | 0.97 | 30 | empty |
| 4 | 154 | 0.82 | 0.98 | 29 | empty |
| 5 | 155 | 0.82 | 0.98 | 27 | empty |
Interfaces
56 interfaces between chains.
- C–G · 4776 Ų buried · 56 hydrogen bonds · protein-protein
- D–H · 4770 Ų buried · 56 hydrogen bonds · protein-protein
- A–E · 4762 Ų buried · 56 hydrogen bonds · protein-protein
- B–F · 4762 Ų buried · 56 hydrogen bonds · protein-protein
- E–M · 1698 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (carboxylation).
Compared structures
- 5NV3 · Structure of Rubisco from Rhodobacter sphaeroides in complex with CABP · the same entry in another collection · chain H against H, 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 P27997
- Every structure of UniProt P27998
- Elsewhere: RCSB PDB 5NV3 · PDBe 5NV3 · UniProt P27997 · UniProt P27998
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