Research workbench
Dypb N246A in complex with manganese
Analyse Dypb N246A in complex with manganese in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HOV
- Type
- protein
- Length
- 925 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dypb
- EC
- 1.11.1.-
- UniProt
- Q0SE24
- Ligands
- HEM, MN, CL
- Pockets
- 10 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Dypb (EC 1.11.1.-) | protein | 308 | 32% helix, 25% strand | Q0SE24 |
| B | Dypb (EC 1.11.1.-) | protein | 309 | 32% helix, 25% strand | Q0SE24 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 3 copies · chains A, B, C
- MN · Manganese (II) ion · metal · 3 copies · chains A, B, C
- CL · Chloride ion · ion · 3 copies · chains A, B, C
- FMT · Formic acid · additive · chains A
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 334 | 0.81 | 0.91 | 39 | HEM, MN |
| 2 | 327 | 0.80 | 0.91 | 39 | HEM, MN |
| 3 | 958 | 0.79 | 0.81 | 118 | HEM, MN |
| 4 | 127 | 0.72 | 0.92 | 36 | empty |
| 5 | 475 | 0.67 | 0.79 | 53 | CL, GOL |
Interfaces
3 interfaces between chains.
- A–B · 1195 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 770 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 381 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4HOV · DypB N246A in complex with manganese · 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 Q0SE24
- Elsewhere: RCSB PDB 4HOV · PDBe 4HOV · UniProt Q0SE24
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