Research workbench
Structure of 5% reduced kpdyp in complex with cyanide
Analyse Structure of 5% reduced kpdyp in complex with cyanide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RPE
- Type
- protein
- Length
- 597 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Iron-dependent peroxidase
- EC
- 1.11.1.-
- UniProt
- A0A0W8ATM9
- Ligands
- HEM, MG, CYN
- Pockets
- 6 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Iron-dependent peroxidase (EC 1.11.1.-) | protein | 299 | 35% helix, 26% strand | A0A0W8ATM9 |
| B | Iron-dependent peroxidase (EC 1.11.1.-) | protein | 298 | 35% helix, 26% strand | A0A0W8ATM9 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- CYN · Cyanide ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 344 | 0.84 | 0.93 | 45 | HEM, CYN |
| 2 | 349 | 0.79 | 0.89 | 39 | HEM, MG, CYN |
| 3 | 496 | 0.71 | 0.81 | 52 | empty |
| 4 | 75 | 0.45 | 0.82 | 17 | empty |
| 5 | 178 | 0.41 | 0.72 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 984 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6RPE · Structure of 5% reduced KpDyP in complex with cyanide · 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 A0A0W8ATM9
- Elsewhere: RCSB PDB 6RPE · PDBe 6RPE · UniProt A0A0W8ATM9
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