Research workbench
Crystal structure of the ATP/MG2+ bound composite dimer of hlyb-nbd
Analyse Crystal structure of the ATP/MG2+ bound composite dimer of hlyb-nbd in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XEF
- Type
- protein
- Length
- 964 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-hemolysin translocation ATP-binding protein hlyb
- UniProt
- P08716
- Ligands
- ATP, MG
- Pockets
- 12 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Alpha-hemolysin translocation ATP-binding protein hlyb | protein | 241 | 35% helix, 24% strand | P08716 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1166 | 0.80 | 0.81 | 109 | MG, ATP |
| 2 | 934 | 0.73 | 0.77 | 94 | MG, ATP |
| 3 | 847 | 0.73 | 0.78 | 87 | MG, ATP |
| 4 | 815 | 0.72 | 0.77 | 76 | MG, ATP |
| 5 | 155 | 0.54 | 0.81 | 26 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1494 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1468 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 274 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 249 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 26 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1XEF · Crystal structure of the ATP/Mg2+ bound composite dimer of HlyB-NBD · the same entry in another collection · chain A against A, TM-score 1.00
- P08716 · AlphaFold monomer V2.0 prediction for alpha-hemolysin translocation ATP-binding protein… · a predicted model of the same protein · chain A against A, TM-score 0.94
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 P08716
- Elsewhere: RCSB PDB 1XEF · PDBe 1XEF · UniProt P08716
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