Research workbench

Core-streptavidin mutant W108F in complex with biotin at pH 7.0

Analyse Core-streptavidin mutant W108F in complex with biotin at pH 7.0 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1SWN
Type: protein
Length: 470 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Core-streptavidin
UniProt: P22629
Ligands: BTN
Pockets: 4 · best druggability 0.72

Structure

x-ray diffraction · 3 distinct chains · 4% helix, 56% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Core-streptavidin	protein	120	3% helix, 56% strand	P22629
B	Core-streptavidin	protein	114	8% helix, 57% strand	P22629
C, D	Core-streptavidin	protein	118	3% helix, 56% strand	P22629

Ligands and binding sites

BTN · Biotin · ligand · 3 copies · chains A, D, B, C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	544	0.72	0.80	73	BTN
2	353	0.68	0.82	51	BTN
3	357	0.62	0.78	42	empty
4	163	0.61	0.83	26	BTN

Interfaces

6 interfaces between chains.

C–D · 1627 Å² buried · 14 hydrogen bonds · protein-protein
A–B · 1584 Å² buried · 15 hydrogen bonds · protein-protein
A–D · 520 Å² buried · 2 hydrogen bonds · protein-protein
B–C · 452 Å² buried · 2 hydrogen bonds · protein-protein
A–C · 181 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

1SWN · Core-streptavidin mutant W108F in complex with biotin at pH 7.0 · 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 1SWN · PDBe 1SWN · UniProt P22629

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