Research workbench
Cryo-electron microscopy structure of a rbcl-RAF1 supercomplex from synechococcus elongatus pcc 7942
Analyse Cryo-electron microscopy structure of a rbcl-RAF1 supercomplex from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SMH
- Type
- protein
- Length
- 5,025 residues
- Chains
- 16
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribulose bisphosphate carboxylase large chain; Rubisco accumulation factor 1 (RAF1)…
- EC
- 4.1.1.39
- UniProt
- Q31NB3, Q31Q05
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 6 distinct chains · 40% helix, 4% 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 | 447 | 36% helix, 13% strand | Q31NB3 |
| I, K, L | Rubisco accumulation factor 1 (RAF1) peptide | protein | 179 | 38% helix, 0% strand | Q31Q05 |
| J | Rubisco accumulation factor 1 (RAF1) peptide | protein | 188 | 37% helix, 0% strand | Q31Q05 |
| M | Rubisco accumulation factor 1 (RAF1) peptide | protein | 180 | 45% helix, 0% strand | Q31Q05 |
| N, O | Rubisco accumulation factor 1 (RAF1) peptide | protein | 181 | 46% helix, 0% strand | Q31Q05 |
| P | Rubisco accumulation factor 1 (RAF1) peptide | protein | 182 | 45% helix, 0% strand | Q31Q05 |
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 | 889 | 0.89 | 0.92 | 136 | empty |
| 2 | 967 | 0.88 | 0.89 | 129 | empty |
| 3 | 886 | 0.87 | 0.90 | 135 | empty |
| 4 | 890 | 0.87 | 0.89 | 115 | empty |
| 5 | 472 | 0.84 | 0.91 | 74 | empty |
Interfaces
40 interfaces between chains.
- B–G · 3256 Ų buried · 40 hydrogen bonds · protein-protein
- A–H · 3246 Ų buried · 29 hydrogen bonds · protein-protein
- D–E · 3246 Ų buried · 29 hydrogen bonds · protein-protein
- C–F · 3225 Ų buried · 31 hydrogen bonds · protein-protein
- B–N · 1288 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 6SMH · Cryo-electron microscopy structure of a RbcL-Raf1 supercomplex from Synechococcus… · the same entry in another collection · chain P against P, 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 Q31NB3
- Every structure of UniProt Q31Q05
- Elsewhere: RCSB PDB 6SMH · PDBe 6SMH · UniProt Q31NB3 · UniProt Q31Q05
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