Research workbench
Crystal structure of pneumococcal surface antigen psaa D280N in the metal-bound, open state
Analyse Crystal structure of pneumococcal surface antigen psaa D280N in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZKA
- Type
- protein
- Length
- 556 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Manganese ABC transporter substrate-binding lipoprotein
- UniProt
- P0A4G2
- Ligands
- MN
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Manganese ABC transporter substrate-binding lipoprotein | protein | 278 | 48% helix, 14% strand | P0A4G2 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 776 | 0.79 | 0.83 | 89 | TRS |
| 2 | 244 | 0.57 | 0.79 | 39 | MN |
| 3 | 197 | 0.56 | 0.80 | 34 | MN |
| 4 | 50 | 0.30 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 822 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3ZKA · Crystal structure of pneumococcal surface antigen psaa D280N in the metal-bound, open… · the same entry in another collection · chain A against A, TM-score 1.00
- P0A4G2 · AlphaFold monomer V2.0 prediction for manganese ABC transporter substrate-binding… · a predicted model of the same protein · 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 P0A4G2
- Elsewhere: RCSB PDB 3ZKA · PDBe 3ZKA · UniProt P0A4G2
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