Research workbench
Structure of the central neat domain, N2, of the listerial HBP2 protein complexed with heme
Analyse Structure of the central neat domain, N2, of the listerial HBP2 protein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MYP
- Type
- protein
- Length
- 238 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Iron-regulated surface determinant protein a
- UniProt
- Q9KGV9
- Ligands
- HEM, ZN
- Pockets
- 1 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 62% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Iron-regulated surface determinant protein a | protein | 121 | 4% helix, 62% strand | Q9KGV9 |
| B | Iron-regulated surface determinant protein a | protein | 117 | 4% helix, 62% strand | Q9KGV9 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
- GOL · Glycerol · additive · 9 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 400 | 0.64 | 0.78 | 39 | HEM |
Interfaces
1 interface between chains.
- A–B · 323 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4MYP · Structure of the central NEAT domain, N2, of the listerial Hbp2 protein complexed with… · 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 Q9KGV9
- Elsewhere: RCSB PDB 4MYP · PDBe 4MYP · UniProt Q9KGV9
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