MolNFT v1 · #191125 · protein

Dithiol-ligand bound to streptavidin

7ZXZ: “Dithiol-ligand bound to streptavidin”. X-ray diffraction, 1 ligand (K9R), 2 pockets (best druggability 0.64). MolNFT v1 #191125 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7ZXZ
Type: protein
Length: 247 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Streptavidin
UniProt: P22629
Ligands: K9R
Pockets: 2 · best druggability 0.64

Structure

x-ray diffraction · 2 distinct chains · 8% helix, 54% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Streptavidin	protein	123	8% helix, 54% strand	P22629
B	Streptavidin	protein	124	8% helix, 54% strand	P22629

Ligands and binding sites

K9R · 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~{R},3~{S})-3-[3,5-bis(sulfanylmethyl)phenyl]-2,4-bis(oxidanylidene)cyclopentyl]pentanamide · ligand · 2 copies · chains A, B
PEG · Di(hydroxyethyl)ether · additive · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	74	0.64	0.91	18	K9R
2	124	0.57	0.83	27	K9R

Interfaces

1 interface between chains.

A–B · 539 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

7ZXZ · dithiol-ligand bound to streptavidin · 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 7ZXZ · PDBe 7ZXZ · UniProt P22629

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