Research workbench
Crystal structure of the protein of unknown function YPO0625 from yersinia pestis
Analyse Crystal structure of the protein of unknown function YPO0625 from yersinia… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7TMU
- Type
- protein
- Length
- 579 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Srpbcc family protein
- UniProt
- A0A3G5LAW0
- Ligands
- K, CL
- Pockets
- 9 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Srpbcc family protein | protein | 144 | 28% helix, 45% strand | A0A3G5LAW0 |
| B | Srpbcc family protein | protein | 145 | 32% helix, 45% strand | A0A3G5LAW0 |
| C | Srpbcc family protein | protein | 146 | 29% helix, 45% strand | A0A3G5LAW0 |
Ligands and binding sites
- K · Potassium ion · metal · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 6 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 5 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 2 copies · chains B, D
- GOL · Glycerol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 140 | 0.68 | 0.88 | 25 | PEG |
| 2 | 152 | 0.66 | 0.87 | 25 | PEG |
| 3 | 167 | 0.64 | 0.84 | 26 | PEG |
| 4 | 151 | 0.62 | 0.84 | 23 | GOL |
| 5 | 419 | 0.56 | 0.73 | 52 | empty |
Interfaces
4 interfaces between chains.
- A–B · 520 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 495 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 459 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 42 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 7TMU · Crystal Structure of the Protein of Unknown Function YPO0625 from Yersinia pestis · the same entry in another collection · chain A against A, 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 A0A3G5LAW0
- Elsewhere: RCSB PDB 7TMU · PDBe 7TMU · UniProt A0A3G5LAW0
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