Research workbench
A zn-mediated tetrahedral protein lattice cage encapsulating a microperoxidase
Analyse A zn-mediated tetrahedral protein lattice cage encapsulating a microperoxidase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3M4C
- Type
- protein
- Length
- 433 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Soluble cytochrome B562; Heme-peptide fragment
- UniProt
- P0ABE7
- Ligands
- HEM, ZN
- Pockets
- 9 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 80% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Soluble cytochrome B562 | protein | 106 | 80% helix, 0% strand | P0ABE7 |
| E | Heme-peptide fragment | protein | 9 | 78% helix, 0% strand | — |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 5 copies · chains A, B, C, D, E
- ZN · Zinc ion · metal · 10 copies · chains A, B, D, C
- ACT · Acetate ion · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 325 | 0.60 | 0.78 | 42 | empty |
| 2 | 161 | 0.60 | 0.83 | 25 | HEM |
| 3 | 150 | 0.58 | 0.82 | 23 | HEM |
| 4 | 285 | 0.57 | 0.77 | 38 | empty |
| 5 | 167 | 0.57 | 0.81 | 25 | HEM |
Interfaces
6 interfaces between chains.
- C–D · 403 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 333 Ų buried · 10 hydrogen bonds · protein-protein
- B–E · 135 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 123 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 123 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 cofactor, 4 covalent (heme attachment, additive adduct).
Compared structures
- 3M4C · A Zn-mediated tetrahedral protein lattice cage encapsulating a microperoxidase · the same entry in another collection · chain E against E, TM-score 1.00
- P0ABE7 · AlphaFold monomer V2.0 prediction for soluble cytochrome B562 (P0ABE7) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P0ABE7
- Elsewhere: RCSB PDB 3M4C · PDBe 3M4C · UniProt P0ABE7
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