Research workbench
The crystal structure of a cbs domain from a putative metal ion transporter bound to AMP from pseudomonas syringae to 1.55A
Analyse The crystal structure of a cbs domain from a putative metal ion transporter… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LFR
- Type
- protein
- Length
- 251 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative metal ion transporter
- UniProt
- Q87VX8
- Ligands
- AMP
- Pockets
- 2 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative metal ion transporter | protein | 123 | 40% helix, 26% strand | Q87VX8 |
| B | Putative metal ion transporter | protein | 128 | 38% helix, 25% strand | Q87VX8 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 304 | 0.61 | 0.79 | 38 | AMP |
| 2 | 290 | 0.59 | 0.78 | 39 | AMP |
Interfaces
1 interface between chains.
- A–B · 1400 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 3LFR · The Crystal Structure of a CBS Domain from a Putative Metal Ion Transporter Bound to AMP… · 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 Q87VX8
- Elsewhere: RCSB PDB 3LFR · PDBe 3LFR · UniProt Q87VX8
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