MolNFT v1 · #188227 · protein
Crystal structure of the soluble domain of the putative ompa -family membrane protein YPO0514 from yersinia pestis
7THW · Putative ompa-family membrane protein: “Crystal structure of the soluble domain of the putative ompa -family membrane protein YPO0514 from yersinia…”. X-ray diffraction, 2 ligands (CA, PO4), 11 pockets (best druggability 0.68).…
- PDB
- 7THW
- Type
- protein
- Length
- 603 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative ompa-family membrane protein
- UniProt
- A0A454Y5W9
- Ligands
- CA, PO4
- Pockets
- 11 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 73% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative ompa-family membrane protein | protein | 158 | 75% helix, 0% strand | A0A454Y5W9 |
| B | Putative ompa-family membrane protein | protein | 144 | 73% helix, 0% strand | A0A454Y5W9 |
| C | Putative ompa-family membrane protein | protein | 155 | 71% helix, 0% strand | A0A454Y5W9 |
| D | Putative ompa-family membrane protein | protein | 146 | 72% helix, 0% strand | A0A454Y5W9 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 925 | 0.68 | 0.74 | 90 | CA |
| 2 | 162 | 0.54 | 0.80 | 27 | empty |
| 3 | 102 | 0.49 | 0.81 | 14 | empty |
| 4 | 69 | 0.42 | 0.81 | 12 | empty |
| 5 | 96 | 0.41 | 0.78 | 23 | empty |
Interfaces
5 interfaces between chains.
- A–C · 793 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 722 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 698 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 177 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 150 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 23 modified (engineered).
Compared structures
- 7THW · Crystal Structure of the Soluble Domain of the Putative OmpA -Family Membrane Protein… · 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 A0A454Y5W9
- Elsewhere: RCSB PDB 7THW · PDBe 7THW · UniProt A0A454Y5W9
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