Research workbench
Crystal structure of trka-N domain of inner membrane protein ybal from escherichia COLI
Analyse Crystal structure of trka-N domain of inner membrane protein ybal from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FWZ
- Type
- protein
- Length
- 275 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inner membrane protein ybal
- UniProt
- P39830
- Ligands
- AMP, MG
- Pockets
- 2 · best druggability 0.34
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Inner membrane protein ybal | protein | 140 | 48% helix, 19% strand | P39830 |
| B | Inner membrane protein ybal | protein | 135 | 49% helix, 20% strand | P39830 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 74 | 0.34 | 0.76 | 21 | AMP |
| 2 | 65 | 0.33 | 0.76 | 19 | AMP |
Interfaces
1 interface between chains.
- A–B · 1430 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified, 2 disulfide (engineered, disulfide).
Compared structures
- 3FWZ · Crystal structure of TrkA-N domain of inner membrane protein ybaL from Escherichia coli · the same entry in another collection · chain A against A, TM-score 1.00
- P39830 · AlphaFold monomer V2.0 prediction for putative CATION/PROTON antiporter ybal (P39830) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P39830
- Elsewhere: RCSB PDB 3FWZ · PDBe 3FWZ · UniProt P39830
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