MolNFT v1 · #164598 · protein

Streptavidin variants harbouring an artificial organocatalyst based cofactor

6T31: “Streptavidin variants harbouring an artificial organocatalyst based cofactor”. X-ray diffraction, 1 ligand (HL9), 2 pockets (best druggability 0.50). MolNFT v1 #164598 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6T31
Type: protein
Length: 246 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Streptavidin
UniProt: P22629
Ligands: HL9
Pockets: 2 · best druggability 0.50

Structure

x-ray diffraction · 2 distinct chains · 4% helix, 54% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Streptavidin	protein	122	2% helix, 54% strand	P22629
B	Streptavidin	protein	124	6% helix, 53% strand	P22629

Ligands and binding sites

HL9 · 5-[(3~{A}~{S},4~{S},6~{A}~{R})-2-oxidanylidene-1,3, 3~{A},4,6,6~{A}-hexahydrothieno[3,4-d]imidazol-4-yl]-~{N}-(1-pyridin-4-ylpiperidin-4-yl)pentanamide · ligand · 2 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	105	0.50	0.81	20	HL9
2	114	0.47	0.79	24	HL9

Interfaces

1 interface between chains.

A–B · 210 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

6T31 · Streptavidin variants harbouring an artificial organocatalyst based cofactor · 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 6T31 · PDBe 6T31 · UniProt P22629

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