MolNFT v1 · #188337 · protein
Crystal structure of the protein of unknown function YPO0625 from yersinia pestis
7TMU · Srpbcc family protein: “Crystal structure of the protein of unknown function YPO0625 from yersinia pestis”. X-ray diffraction, 2 ligands (K, CL), 9 pockets (best druggability 0.68). MolNFT v1 #188337 on GenesisL1: 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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