Research workbench
Crystal structure of a putative extracellular heme-binding protein (DESPIG_02683) from desulfovibrio piger atcc 29098 at 1.24 a resolution
Analyse Crystal structure of a putative extracellular heme-binding protein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NKP
- Type
- protein
- Length
- 560 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative extracellular heme-binding protein
- UniProt
- B6WX57
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.59
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative extracellular heme-binding protein | protein | 138 | 45% helix, 19% strand | B6WX57 |
| B | Putative extracellular heme-binding protein | protein | 140 | 43% helix, 19% strand | B6WX57 |
| C | Putative extracellular heme-binding protein | protein | 145 | 43% helix, 19% strand | B6WX57 |
| D | Putative extracellular heme-binding protein | protein | 137 | 45% helix, 20% strand | B6WX57 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains A, C, D
- GOL · Glycerol · additive · 7 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 263 | 0.59 | 0.79 | 32 | empty |
| 2 | 174 | 0.47 | 0.75 | 18 | GOL |
| 3 | 107 | 0.47 | 0.80 | 24 | empty |
| 4 | 161 | 0.45 | 0.75 | 20 | GOL |
Interfaces
3 interfaces between chains.
- C–D · 945 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 941 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 775 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 4NKP · Crystal structure of a putative extracellular heme-binding protein (DESPIG_02683) from… · 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 B6WX57
- Elsewhere: RCSB PDB 4NKP · PDBe 4NKP · UniProt B6WX57
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