MolNFT v1 · #22150 · protein

Core-streptavidin mutant W120F in complex with biotin at pH 7.5

1SWP: “Core-streptavidin mutant W120F in complex with biotin at pH 7.5”. X-ray diffraction, 2 ligands (BTN, BTQ), 7 pockets (best druggability 0.68). MolNFT v1 #22150 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1SWP
Type: protein
Length: 468 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Core-streptavidin
UniProt: P22629
Ligands: BTN, BTQ
Pockets: 7 · best druggability 0.68

Structure

x-ray diffraction · 1 distinct chain · 5% helix, 58% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Core-streptavidin	protein	117	5% helix, 58% strand	P22629

Ligands and binding sites

BTN · Biotin · ligand · 3 copies · chains A, D, B, C
BTQ · Epi-biotin · ligand · chains 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	288	0.68	0.83	48	BTN, BTQ
2	145	0.59	0.83	28	BTN
3	223	0.58	0.80	34	empty
4	138	0.58	0.83	25	BTN
5	173	0.57	0.82	24	empty

Interfaces

6 interfaces between chains.

C–D · 1623 Å² buried · 23 hydrogen bonds · protein-protein
A–B · 1587 Å² buried · 26 hydrogen bonds · protein-protein
B–C · 484 Å² buried · 2 hydrogen bonds · protein-protein
A–D · 482 Å² buried · 2 hydrogen bonds · protein-protein
B–D · 196 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

1SWP · Core-streptavidin mutant W120F in complex with biotin at pH 7.5 · 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 1SWP · PDBe 1SWP · UniProt P22629

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