MolNFT v1 · #114204 · protein

Crystal structure of ALIS3-streptavidin complex

5B5F: “Crystal structure of ALIS3-streptavidin complex”. X-ray diffraction, 1 ligand (6F3), 8 pockets (best druggability 0.59). MolNFT v1 #114204 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5B5F
Type: protein
Length: 480 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Streptavidin
UniProt: P22629
Ligands: 6F3
Pockets: 8 · best druggability 0.59

Structure

x-ray diffraction · 1 distinct chain · 5% helix, 57% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Streptavidin	protein	120	5% helix, 57% strand	P22629

Ligands and binding sites

6F3 · N-methyl-3-(4-oxo-4,5-dihydrofuro[3,2-c]pyridin-2-yl)benzenesulfonamide · ligand · 4 copies · chains A, C, B, 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	116	0.59	0.85	25	6F3
2	163	0.54	0.80	26	empty
3	174	0.54	0.80	26	empty
4	174	0.52	0.79	32	empty
5	171	0.52	0.79	26	empty

Interfaces

6 interfaces between chains.

A–D · 1624 Å² buried · 32 hydrogen bonds · protein-protein
B–C · 1618 Å² buried · 28 hydrogen bonds · protein-protein
A–C · 484 Å² buried · 2 hydrogen bonds · protein-protein
B–D · 416 Å² buried · 2 hydrogen bonds · protein-protein
C–D · 212 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

5B5F · Crystal structure of ALiS3-Streptavidin complex · 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 5B5F · PDBe 5B5F · UniProt P22629

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