MolNFT v1 · #155926 · protein

Rapid crystallization of streptavidin using charged peptides

6LNG: “Rapid crystallization of streptavidin using charged peptides”. X-ray diffraction, 5 pockets (best druggability 0.72). MolNFT v1 #155926 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6LNG
Type: protein
Length: 732 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Streptavidin
UniProt: P22629
Pockets: 5 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 5% helix, 56% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Streptavidin	protein	122	5% helix, 56% strand	P22629

Ligands and binding sites

GOL · Glycerol · additive · 6 copies · chains A, D, B, C, E, F

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

Pockets

5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	731	0.72	0.78	82	GOL
2	552	0.66	0.77	60	GOL
3	352	0.63	0.79	44	GOL
4	343	0.56	0.75	42	GOL
5	187	0.52	0.77	23	GOL

Interfaces

9 interfaces between chains.

C–D · 1674 Å² buried · 29 hydrogen bonds · protein-protein
A–B · 1642 Å² buried · 30 hydrogen bonds · protein-protein
B–C · 395 Å² buried · 2 hydrogen bonds · protein-protein
E–F · 394 Å² buried · 2 hydrogen bonds · protein-protein
A–D · 393 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

6LNG · Rapid crystallization of streptavidin using charged peptides · 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 6LNG · PDBe 6LNG · UniProt P22629

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