Research workbench
Escherichia COLI bacterioferritin substituted with zinc protoporphyrin IX (zn absorption edge X-ray data)
Analyse Escherichia COLI bacterioferritin substituted with zinc protoporphyrin IX (zn… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6P8L
- Type
- protein
- Length
- 1,884 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bacterioferritin
- EC
- 1.16.3.1
- UniProt
- P0ABD3
- Ligands
- ZNH, ZN, NA
- 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 (EC 1.16.3.1) | protein | 157 | 78% helix, 0% strand | P0ABD3 |
Ligands and binding sites
- ZNH · Protoporphyrin IX containing Zn · ligand · 6 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- ZN · Zinc ion · metal · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- NA · Sodium ion · metal · 4 copies · chains A, C, B, G, J, K, D, H, F, L
- MLI · Malonate ion · additive · 28 copies · chains A, J, B, C, H, D, E, F, I, G, L, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 203 | 0.73 | 0.88 | 31 | ZNH |
| 2 | 223 | 0.73 | 0.87 | 31 | ZNH |
| 3 | 240 | 0.71 | 0.86 | 25 | empty |
| 4 | 212 | 0.70 | 0.86 | 34 | ZNH |
| 5 | 212 | 0.70 | 0.86 | 35 | ZNH |
Interfaces
24 interfaces between chains.
- I–J · 973 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 971 Ų buried · 14 hydrogen bonds · protein-protein
- K–L · 969 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 964 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 963 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6P8L · Escherichia coli Bacterioferritin Substituted with Zinc Protoporphyrin IX (Zn Absorption… · 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 6P8L · PDBe 6P8L · UniProt P0ABD3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.