MolNFT v1 · #100474 · protein
Structure of the central neat domain, N2, of the listerial HBP2 protein complexed with heme
4MYP · Iron-regulated surface determinant protein a: “Structure of the central neat domain, N2, of the listerial HBP2 protein complexed with heme”. X-ray diffraction, 2 ligands (HEM, ZN), 1 pocket (best druggability 0.64). MolNFT v1…
- 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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