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Crystal structure of the core streptavidin mutant V212 (Y22S/N23D/S27D/S45N/Y83S/R84K/E101D/R103K/E116N) complexed with bis iminobiotin long tail (bis-imntail) at 1.3 a resolution

Analyse Crystal structure of the core streptavidin mutant V212… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3X00
Type: protein
Length: 496 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Streptavidin
UniProt: P22629
Ligands: ZOF, EDN
Pockets: 8 · best druggability 0.55

Structure

x-ray diffraction · 1 distinct chain · 12% helix, 54% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Streptavidin	protein	124	12% helix, 54% strand	P22629

Ligands and binding sites

ZOF · 6-({5-[(2E,3aS,4S,6aR)-2-iminohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoyl}amino)hexanoic acid · ligand · 4 copies · chains A, D, B, C
EDN · Ethane-1,2-diamine · ligand · 2 copies · chains B, C, A, D

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

Pockets

8 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	150	0.55	0.82	22	empty
2	162	0.54	0.80	26	empty
3	171	0.54	0.80	25	empty
4	153	0.52	0.79	18	ZOF
5	155	0.51	0.79	25	empty

Interfaces

6 interfaces between chains.

C–D · 1622 Å² buried · 25 hydrogen bonds · protein-protein
A–B · 1598 Å² buried · 28 hydrogen bonds · protein-protein
B–C · 410 Å² buried · 2 hydrogen bonds · protein-protein
A–D · 410 Å² buried · 2 hydrogen bonds · protein-protein
A–C · 218 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

3X00 · Crystal structure of the core streptavidin mutant V212… · 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 3X00 · PDBe 3X00 · UniProt P22629

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