Research workbench
Structure of the repeat unit in the network formed by ccmm and rubisco from synechococcus elongatus
Analyse Structure of the repeat unit in the network formed by ccmm and rubisco from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HBC
- Type
- protein
- Length
- 1,178 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carbon dioxide concentrating mechanism protein ccmm; Ribulose bisphosphate carboxylase…
- EC
- 4.1.1.39
- UniProt
- Q03513, Q31NB3, Q31NB2
- Pockets
- 18 · best druggability 0.80
Structure
electron microscopy · 3 distinct chains · 40% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Carbon dioxide concentrating mechanism protein ccmm | protein | 86 | 36% helix, 30% strand | Q03513 |
| B, C | Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) | protein | 440 | 44% helix, 18% strand | Q31NB3 |
| D, E | Ribulose 1,5-bisphosphate carboxylase small subunit (EC 4.1.1.39) | protein | 106 | 25% helix, 26% strand | Q31NB2 |
Pockets
18 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1024 | 0.80 | 0.82 | 90 | empty |
| 2 | 711 | 0.73 | 0.79 | 82 | empty |
| 3 | 363 | 0.62 | 0.78 | 61 | empty |
| 4 | 143 | 0.61 | 0.85 | 32 | empty |
| 5 | 124 | 0.59 | 0.85 | 22 | empty |
Interfaces
8 interfaces between chains.
- B–D · 1645 Ų buried · 21 hydrogen bonds · protein-protein
- C–E · 1642 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 569 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 497 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 390 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6HBC · Structure of the repeat unit in the network formed by CcmM and Rubisco from Synechococcus… · the same entry in another collection · chain E against E, TM-score 1.00
- Q31NB3 · AlphaFold monomer V2.0 prediction for ribulose bisphosphate carboxylase large chain… · a predicted model of the same protein · chain B against A, TM-score 0.99
- Q03513 · AlphaFold monomer V2.0 prediction for carboxysome assembly protein ccmm (Q03513) · a predicted model of the same protein · chain A against A, TM-score 0.98
- Q31NB2 · AlphaFold monomer V2.0 prediction for ribulose bisphosphate carboxylase small subunit… · a predicted model of the same protein · chain D against A, TM-score 0.97
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 Q03513
- Every structure of UniProt Q31NB3
- Every structure of UniProt Q31NB2
- Elsewhere: RCSB PDB 6HBC · PDBe 6HBC · UniProt Q03513 · UniProt Q31NB3 · UniProt Q31NB2
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