MolNFT v1 · #22139 · protein

Apo-core-streptavidin in complex with biotin at pH 4.5

1SWE: “Apo-core-streptavidin in complex with biotin at pH 4.5”. X-ray diffraction, 1 ligand (BTN), 7 pockets (best druggability 0.67). MolNFT v1 #22139 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1SWE
Type: protein
Length: 471 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Streptavidin
UniProt: P22629
Ligands: BTN
Pockets: 7 · best druggability 0.67

Structure

x-ray diffraction · 2 distinct chains · 4% helix, 57% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Streptavidin	protein	117	5% helix, 57% strand	P22629
B, C, D	Streptavidin	protein	118	3% helix, 57% 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

7 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	260	0.67	0.83	49	BTN
2	140	0.60	0.84	26	BTN
3	136	0.58	0.83	26	BTN
4	150	0.56	0.82	29	empty
5	210	0.55	0.79	32	empty

Interfaces

6 interfaces between chains.

C–D · 1642 Å² buried · 25 hydrogen bonds · protein-protein
A–B · 1613 Å² buried · 28 hydrogen bonds · protein-protein
B–C · 531 Å² buried · 4 hydrogen bonds · protein-protein
A–D · 527 Å² buried · 2 hydrogen bonds · protein-protein
B–D · 209 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

1SWE · Apo-core-streptavidin in complex with biotin at pH 4.5 · 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 1SWE · PDBe 1SWE · UniProt P22629

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