Research workbench
Structure of chlorite dismutase-like protein from listeria monocytogenes
Analyse Structure of chlorite dismutase-like protein from listeria monocytogenes in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WWS
- Type
- protein
- Length
- 1,198 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
- K
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Putative heme-dependent peroxidase LMO2113 (EC 1.11.1.-) | protein | 247 | 38% helix, 32% strand | Q8Y5F1 |
| B | Putative heme-dependent peroxidase LMO2113 (EC 1.11.1.-) | protein | 234 | 44% helix, 32% strand | Q8Y5F1 |
| C | Putative heme-dependent peroxidase LMO2113 (EC 1.11.1.-) | protein | 235 | 40% helix, 32% strand | Q8Y5F1 |
| D | Putative heme-dependent peroxidase LMO2113 (EC 1.11.1.-) | protein | 235 | 41% helix, 32% strand | Q8Y5F1 |
Ligands and binding sites
- K · Potassium ion · metal · 5 copies · chains A, B, C, E, D
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 | 493 | 0.77 | 0.85 | 50 | empty |
| 2 | 569 | 0.77 | 0.83 | 55 | empty |
| 3 | 649 | 0.73 | 0.80 | 57 | empty |
| 4 | 644 | 0.71 | 0.78 | 55 | empty |
| 5 | 769 | 0.70 | 0.77 | 94 | empty |
Interfaces
5 interfaces between chains.
- A–C · 1753 Ų buried · 32 hydrogen bonds · protein-protein
- B–E · 1704 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 1667 Ų buried · 29 hydrogen bonds · protein-protein
- D–E · 1665 Ų buried · 32 hydrogen bonds · protein-protein
- C–D · 1655 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 4WWS · Structure of Chlorite dismutase-like Protein from Listeria monocytogenes · 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 C 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 4WWS · PDBe 4WWS · UniProt Q8Y5F1
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