MolNFT v1 · #52330 · protein
The binding of heme and zinc in escherichia COLI bacterioferritin
2VXI: “The binding of heme and zinc in escherichia COLI bacterioferritin”. X-ray diffraction, 3 ligands (HEM, ZN, SO4), 20 pockets (best druggability 0.73). MolNFT v1 #52330 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2VXI
- Type
- protein
- Length
- 1,884 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bacterioferritin
- UniProt
- P0ABD3
- Ligands
- HEM, ZN, SO4
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | Bacterioferritin | protein | 157 | 78% helix, 0% strand | P0ABD3 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- ZN · Zinc ion · metal · 24 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- SO4 · Sulfate ion · ion · 29 copies · chains A, B, D, F, C, K, E, G, H, J, L, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 222 | 0.73 | 0.88 | 33 | HEM |
| 2 | 206 | 0.72 | 0.87 | 32 | HEM |
| 3 | 222 | 0.71 | 0.86 | 33 | HEM |
| 4 | 212 | 0.70 | 0.86 | 29 | HEM |
| 5 | 217 | 0.70 | 0.86 | 32 | HEM |
Interfaces
24 interfaces between chains.
- I–J · 961 Ų buried · 16 hydrogen bonds · protein-protein
- G–H · 960 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 958 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 958 Ų buried · 18 hydrogen bonds · protein-protein
- E–F · 957 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 2VXI · The binding of heme and zinc in Escherichia coli Bacterioferritin · the same entry in another collection · chain L against L, 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 P0ABD3
- Elsewhere: RCSB PDB 2VXI · PDBe 2VXI · UniProt P0ABD3
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