Research workbench
X-ray generated OXYFERROUS/WATER mixed complex of dtpa from streptomyces lividans
Analyse X-ray generated OXYFERROUS/WATER mixed complex of dtpa from streptomyces… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MJH
- Type
- protein
- Length
- 736 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dye type peroxidase a
- UniProt
- A0A076MAJ9
- Ligands
- HEM, OXY
- Pockets
- 12 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dye type peroxidase a | protein | 368 | 29% helix, 23% strand | A0A076MAJ9 |
| B | Dye type peroxidase a | protein | 368 | 27% helix, 23% strand | A0A076MAJ9 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- OXY · Oxygen molecule · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 312 | 0.83 | 0.93 | 42 | HEM, OXY |
| 2 | 333 | 0.81 | 0.91 | 44 | HEM, OXY |
| 3 | 394 | 0.62 | 0.77 | 56 | empty |
| 4 | 363 | 0.61 | 0.77 | 45 | empty |
| 5 | 124 | 0.53 | 0.82 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 2712 Ų buried · 45 hydrogen bonds · protein-protein
Compared structures
- 5MJH · X-ray generated oxyferrous/water mixed complex of DtpA from Streptomyces lividans · 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 A0A076MAJ9
- Elsewhere: RCSB PDB 5MJH · PDBe 5MJH · UniProt A0A076MAJ9
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