MolNFT v1 · #162988 · protein
Structure of ferrous kpdyp in complex with cyanide
6RPD · Iron-dependent peroxidase: “Structure of ferrous kpdyp in complex with cyanide”. X-ray diffraction, 3 ligands (HEM, MG, CYN), 7 pockets (best druggability 0.82). MolNFT v1 #162988 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6RPD
- 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
- 7 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Iron-dependent peroxidase (EC 1.11.1.-) | protein | 299 | 33% helix, 26% strand | A0A0W8ATM9 |
| B | Iron-dependent peroxidase (EC 1.11.1.-) | protein | 298 | 34% 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 · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 296 | 0.82 | 0.93 | 40 | HEM, CYN |
| 2 | 289 | 0.81 | 0.92 | 39 | HEM, CYN |
| 3 | 414 | 0.69 | 0.81 | 36 | GOL |
| 4 | 72 | 0.50 | 0.85 | 15 | GOL |
| 5 | 123 | 0.48 | 0.80 | 26 | GOL |
Interfaces
1 interface between chains.
- A–B · 1020 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6RPD · Structure of ferrous 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 6RPD · PDBe 6RPD · UniProt A0A0W8ATM9
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