MolNFT v1 · #149343 · protein
Structure of coproheme decarboxylase from listeria monocytogenes during turnover
6FXQ · Putative heme-dependent peroxidase LMO2113: “Structure of coproheme decarboxylase from listeria monocytogenes during turnover”. X-ray diffraction, 3 ligands (FEC, VOV, NA), 20 pockets (best druggability 0.77). MolNFT v1 #149343 on…
- PDB
- 6FXQ
- Type
- protein
- Length
- 1,203 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative heme-dependent peroxidase LMO2113
- EC
- 1.11.1.-
- UniProt
- Q8Y5F1
- Ligands
- FEC, VOV, NA
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 5 distinct chains · 41% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative heme-dependent peroxidase LMO2113 (EC 1.11.1.-) | protein | 248 | 40% helix, 31% strand | Q8Y5F1 |
| B | Putative heme-dependent peroxidase LMO2113 (EC 1.11.1.-) | protein | 233 | 42% helix, 32% strand | Q8Y5F1 |
| C | Putative heme-dependent peroxidase LMO2113 (EC 1.11.1.-) | protein | 237 | 41% helix, 32% strand | Q8Y5F1 |
| D | Putative heme-dependent peroxidase LMO2113 (EC 1.11.1.-) | protein | 250 | 40% helix, 31% strand | Q8Y5F1 |
| E | Putative heme-dependent peroxidase LMO2113 (EC 1.11.1.-) | protein | 235 | 41% helix, 33% strand | Q8Y5F1 |
Ligands and binding sites
- FEC · 1,3,5,8-tetramethyl-porphine-2,4,6,7-tetrapropionic acid ferrous complex · ligand · 5 copies · chains A, B, C, D, E
- VOV · harderoheme (III) · ligand · 5 copies · chains A, B, C, D, E
- NA · Sodium ion · metal · 5 copies · chains A, B, C, E, D
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 4 copies · chains A, C, B, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 523 | 0.77 | 0.84 | 48 | FEC, VOV |
| 2 | 530 | 0.77 | 0.84 | 58 | FEC, VOV |
| 3 | 405 | 0.76 | 0.85 | 40 | FEC, VOV |
| 4 | 511 | 0.75 | 0.83 | 46 | FEC, VOV |
| 5 | 519 | 0.73 | 0.81 | 47 | FEC, VOV |
Interfaces
5 interfaces between chains.
- D–E · 1820 Ų buried · 37 hydrogen bonds · protein-protein
- A–C · 1820 Ų buried · 36 hydrogen bonds · protein-protein
- C–D · 1806 Ų buried · 34 hydrogen bonds · protein-protein
- B–E · 1724 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 1681 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 6FXQ · Structure of coproheme decarboxylase from Listeria monocytogenes during turnover · the same entry in another collection · chain E against E, TM-score 1.00
- Q8Y5F1 · AlphaFold monomer V2.0 prediction for coproheme decarboxylase (Q8Y5F1) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q8Y5F1
- Elsewhere: RCSB PDB 6FXQ · PDBe 6FXQ · UniProt Q8Y5F1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.