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Crystal structural of native spas C-terminal domain
Analyse Crystal structural of native spas C-terminal domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3C01
- Type
- protein
- Length
- 427 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Surface presentation of antigens protein spas
- UniProt
- P40702
- Ligands
- CYS, SO4
- Pockets
- 3 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Surface presentation of antigens protein spas | protein | 20 | 40% helix, 20% strand | P40702 |
| E | Surface presentation of antigens protein spas | protein | 88 | 50% helix, 19% strand | P40702 |
| F, G, H | Surface presentation of antigens protein spas | protein | 87 | 51% helix, 26% strand | P40702 |
| C, D | Surface presentation of antigens protein spas | protein | 19 | 42% helix, 21% strand | P40702 |
Ligands and binding sites
- CYS · Cysteine · ligand · 4 copies · chains E, B, F, G, D, H
- SO4 · Sulfate ion · ion · 5 copies · chains A, E, F, G, H
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 977 | 0.76 | 0.79 | 67 | CYS |
| 2 | 334 | 0.72 | 0.84 | 37 | CYS |
| 3 | 51 | 0.23 | 0.72 | 15 | empty |
Interfaces
13 interfaces between chains.
- A–E · 1224 Ų buried · 21 hydrogen bonds · protein-protein
- B–F · 1216 Ų buried · 19 hydrogen bonds · protein-protein
- D–H · 1212 Ų buried · 18 hydrogen bonds · protein-protein
- C–G · 1186 Ų buried · 19 hydrogen bonds · protein-protein
- E–F · 348 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3C01 · Crystal structural of native SpaS C-terminal domain · the same entry in another collection · chain D against D, TM-score 1.00
- P40702 · AlphaFold monomer V2.0 prediction for surface presentation of antigens protein spas… · a predicted model of the same protein · chain G against A, TM-score 0.96
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 P40702
- Elsewhere: RCSB PDB 3C01 · PDBe 3C01 · UniProt P40702
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