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Biotin-bound streptavidin

Analyse Biotin-bound streptavidin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6J6J
Type: protein
Length: 476 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Streptavidin
UniProt: P22629
Ligands: BTN
Pockets: 6 · best druggability 0.69

Structure

electron microscopy · 1 distinct chain · 0% helix, 55% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Streptavidin	protein	119	0% helix, 55% strand	P22629

Ligands and binding sites

BTN · Biotin · ligand · 4 copies · chains A, D, B, C

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

Pockets

6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	354	0.69	0.82	55	BTN
2	156	0.69	0.88	26	BTN
3	171	0.67	0.86	30	BTN
4	158	0.66	0.86	28	BTN
5	320	0.64	0.80	55	empty

Interfaces

6 interfaces between chains.

A–B · 1508 Å² buried · 12 hydrogen bonds · protein-protein
C–D · 1505 Å² buried · 12 hydrogen bonds · protein-protein
A–D · 516 Å² buried · 2 hydrogen bonds · protein-protein
B–C · 510 Å² buried · 2 hydrogen bonds · protein-protein
B–D · 210 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

6J6J · Biotin-bound streptavidin · 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 6J6J · PDBe 6J6J · UniProt P22629

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