Research workbench
Structure of thermotoga maritima smpb
Analyse Structure of thermotoga maritima smpb in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LJP
- Type
- protein
- Length
- 419 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ssra-binding protein
- UniProt
- P56944
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 22% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ssra-binding protein | protein | 135 | 20% helix, 42% strand | P56944 |
| B | Ssra-binding protein | protein | 133 | 20% helix, 44% strand | P56944 |
| C | Ssra-binding protein | protein | 151 | 26% helix, 36% strand | P56944 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 7 copies · chains A, C, B
- DIO · 1,4-diethylene dioxide · additive · 10 copies · chains A, B, C
- GOL · Glycerol · additive · 5 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 876 | 0.72 | 0.77 | 87 | DIO, SO4, GOL |
| 2 | 152 | 0.47 | 0.77 | 25 | GOL |
| 3 | 62 | 0.32 | 0.76 | 18 | empty |
| 4 | 65 | 0.29 | 0.73 | 12 | empty |
Interfaces
3 interfaces between chains.
- A–C · 779 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 486 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 91 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
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 P56944
- Elsewhere: RCSB PDB 7LJP · PDBe 7LJP · UniProt P56944
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