Research workbench
Streptavidin iron-porphyrin
Analyse Streptavidin iron-porphyrin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ZOF
- Type
- protein
- Length
- 490 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Streptavidin
- UniProt
- P22629
- Ligands
- JLL, FE
- Pockets
- 7 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Streptavidin | protein | 122 | 8% helix, 54% strand | P22629 |
| B, C | Streptavidin | protein | 123 | 8% helix, 54% strand | P22629 |
Ligands and binding sites
- JLL · (2R)-2-[5-[(3aS,4S,6aR)-2-oxidanylidene-1,3,3a,4,6,6a-hexahydrothieno[3,4-d]imidazol-4-yl]pentanoylamino]-3-[[(5Z,10Z,14Z,19Z)-15-[[[(2R)-2-[5-[(3aS,4S,6aR)-2-oxidanylidene-1,3,3a,4,6,6a-hexahydrothieno[3,4-d]imidazol-4-yl]pentanoylamino]-3-sulfo-propanoyl]amino]methyl]-1,4,21,23-tetrahydroporphyrin-5-yl]methylamino]-3-oxidanylidene-propane-1-sulfonic acid · ligand · 2 copies · chains A, C, B, D
- FE · Fe (III) ion · metal · 2 copies
- IMD · Imidazole · additive · 4 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 307 | 0.62 | 0.80 | 53 | empty |
| 2 | 105 | 0.61 | 0.87 | 25 | IMD |
| 3 | 94 | 0.61 | 0.87 | 20 | empty |
| 4 | 116 | 0.58 | 0.84 | 25 | empty |
| 5 | 107 | 0.57 | 0.84 | 29 | IMD |
Interfaces
6 interfaces between chains.
- A–B · 1665 Ų buried · 32 hydrogen bonds · protein-protein
- C–D · 1652 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 542 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 541 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 211 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 7ZOF · Streptavidin Iron-Porphyrin · 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 P22629
- Elsewhere: RCSB PDB 7ZOF · PDBe 7ZOF · UniProt P22629
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