Research workbench
Cryo-EM structure of rubisco assembly intermediate RBCL8RAF18RBCX16
Analyse Cryo-EM structure of rubisco assembly intermediate RBCL8RAF18RBCX16 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7XSD
- Type
- protein
- Length
- 6,272 residues
- Chains
- 32
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rubisco chaperone rbcx; Rubisco accumulation factor 1; Ribulose bisphosphate carboxylase…
- EC
- 4.1.1.39
- UniProt
- O86418, Q8YLP6, P00879
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 4 distinct chains · 45% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 5, 7, 1, 3, Q, S, U, W | Rubisco chaperone rbcx | protein | 101 | 63% helix, 0% strand | O86418 |
| 6, 8, 2, 4, R, T, V, X | Rubisco chaperone rbcx | protein | 111 | 76% helix, 0% strand | O86418 |
| O, P, M, N, I, J, K, L | Rubisco accumulation factor 1 | protein | 178 | 59% helix, 0% strand | Q8YLP6 |
| G, H, E, F, A, B, C, D | Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) | protein | 394 | 26% helix, 13% strand | P00879 |
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 | 1106 | 0.84 | 0.85 | 159 | empty |
| 2 | 713 | 0.81 | 0.85 | 87 | empty |
| 3 | 639 | 0.81 | 0.86 | 67 | empty |
| 4 | 825 | 0.81 | 0.84 | 72 | empty |
| 5 | 650 | 0.81 | 0.85 | 75 | empty |
Interfaces
95 interfaces between chains.
- S–T · 2089 Ų buried · 22 hydrogen bonds · protein-protein
- U–V · 2074 Ų buried · 22 hydrogen bonds · protein-protein
- 3–4 · 2071 Ų buried · 20 hydrogen bonds · protein-protein
- Q–R · 2069 Ų buried · 28 hydrogen bonds · protein-protein
- 5–6 · 2066 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 7XSD · Cryo-EM structure of RuBisCO assembly intermediate RbcL8Raf18RbcX16 · the same entry in another collection · chain O against O, 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 O86418
- Every structure of UniProt Q8YLP6
- Every structure of UniProt P00879
- Elsewhere: RCSB PDB 7XSD · PDBe 7XSD · UniProt O86418 · UniProt Q8YLP6 · UniProt P00879
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