Research workbench
The structure of nostoc sp. pcc 7120 ccml
Analyse The structure of nostoc sp. pcc 7120 ccml in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4N8X
- Type
- protein
- Length
- 2,928 residues
- Chains
- 30
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carbon dioxide concentrating mechanism protein
- UniProt
- Q8YYI2
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 5 distinct chains · 9% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1, 3, B, P | Carbon dioxide concentrating mechanism protein | protein | 99 | 9% helix, 52% strand | Q8YYI2 |
| 2, J, O | Carbon dioxide concentrating mechanism protein | protein | 96 | 9% helix, 52% strand | Q8YYI2 |
| 4, A, C, D, F, H, I, K, L, M, N, R, S, V, X, Z | Carbon dioxide concentrating mechanism protein | protein | 98 | 9% helix, 49% strand | Q8YYI2 |
| E, G, Q, U, W, Y | Carbon dioxide concentrating mechanism protein | protein | 97 | 8% helix, 51% strand | Q8YYI2 |
| T | Carbon dioxide concentrating mechanism protein | protein | 94 | 9% helix, 48% strand | Q8YYI2 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains A, R
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 | 1018 | 0.82 | 0.84 | 112 | empty |
| 2 | 833 | 0.77 | 0.81 | 77 | empty |
| 3 | 787 | 0.77 | 0.81 | 98 | empty |
| 4 | 803 | 0.76 | 0.80 | 72 | empty |
| 5 | 840 | 0.76 | 0.80 | 87 | empty |
Interfaces
83 interfaces between chains.
- S–T · 1330 Ų buried · 32 hydrogen bonds · protein-protein
- D–E · 1325 Ų buried · 26 hydrogen bonds · protein-protein
- G–H · 1306 Ų buried · 28 hydrogen bonds · protein-protein
- A–E · 1303 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 1302 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 4N8X · The structure of Nostoc sp. PCC 7120 CcmL · 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 Q8YYI2
- Elsewhere: RCSB PDB 4N8X · PDBe 4N8X · UniProt Q8YYI2
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