MolNFT v1 · #137257 · protein
Crystal structure of heme-containing dyp type peroxidase from enterobacter lignolyticus
5VJ0 · Dyp-type peroxidase family: “Crystal structure of heme-containing dyp type peroxidase from enterobacter lignolyticus”. X-ray diffraction, 1 ligand (HEM), 19 pockets (best druggability 0.80). MolNFT v1 #137257 on GenesisL1: 3D…
- PDB
- 5VJ0
- Type
- protein
- Length
- 1,194 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dyp-type peroxidase family
- UniProt
- E3G9I4
- Ligands
- HEM
- Pockets
- 19 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Dyp-type peroxidase family | protein | 298 | 33% helix, 26% strand | E3G9I4 |
| D | Dyp-type peroxidase family | protein | 300 | 31% helix, 26% strand | E3G9I4 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 334 | 0.80 | 0.90 | 40 | HEM |
| 2 | 341 | 0.80 | 0.90 | 38 | HEM |
| 3 | 1193 | 0.80 | 0.81 | 104 | empty |
| 4 | 338 | 0.80 | 0.90 | 38 | HEM |
| 5 | 341 | 0.79 | 0.89 | 41 | HEM |
Interfaces
5 interfaces between chains.
- A–B · 1014 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1005 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 441 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 393 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 170 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5VJ0 · Crystal Structure of heme-containing DyP Type Peroxidase from Enterobacter lignolyticus · 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 E3G9I4
- Elsewhere: RCSB PDB 5VJ0 · PDBe 5VJ0 · UniProt E3G9I4
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