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Crystal structure of a putative membrane protein of unknown function (yfdx) from klebsiella pneumoniae subsp. at 1.65 a resolution
Analyse Crystal structure of a putative membrane protein of unknown function (yfdx)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DZA
- Type
- protein
- Length
- 711 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized putative membrane protein
- UniProt
- A6TE93
- Ligands
- ZN
- Pockets
- 13 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 59% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Uncharacterized putative membrane protein | protein | 180 | 57% helix, 15% strand | A6TE93 |
| C | Uncharacterized putative membrane protein | protein | 175 | 59% helix, 16% strand | A6TE93 |
| D | Uncharacterized putative membrane protein | protein | 176 | 60% helix, 15% strand | A6TE93 |
Ligands and binding sites
- ZN · Zinc ion · metal · 10 copies · chains A, B, D, C
- EDO · 1,2-ethanediol · additive · 24 copies · chains A, D, B, C
- ACT · Acetate ion · additive · 5 copies · chains B, A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1104 | 0.78 | 0.79 | 87 | EDO |
| 2 | 91 | 0.63 | 0.90 | 24 | EDO |
| 3 | 88 | 0.61 | 0.89 | 24 | EDO |
| 4 | 261 | 0.61 | 0.80 | 29 | empty |
| 5 | 82 | 0.60 | 0.89 | 21 | EDO |
Interfaces
6 interfaces between chains.
- A–B · 2791 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 2569 Ų buried · 35 hydrogen bonds · protein-protein
- A–D · 1300 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1293 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 120 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 3DZA · Crystal structure of a putative membrane protein of unknown function (yfdx) from… · 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 A6TE93
- Elsewhere: RCSB PDB 3DZA · PDBe 3DZA · UniProt A6TE93
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