MolNFT v1 · #111592 · protein

Structure of D128N streptavidin

4YVB: “Structure of D128N streptavidin”. X-ray diffraction, 1 ligand (BTN), 8 pockets (best druggability 0.61). MolNFT v1 #111592 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4YVB
Type: protein
Length: 477 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Streptavidin
UniProt: P22629
Ligands: BTN
Pockets: 8 · best druggability 0.61

Structure

x-ray diffraction · 3 distinct chains · 3% helix, 56% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Streptavidin	protein	119	3% helix, 56% strand	P22629
B, D	Streptavidin	protein	120	3% helix, 56% strand	P22629
C	Streptavidin	protein	118	5% helix, 57% strand	P22629

Ligands and binding sites

BTN · Biotin · ligand · 4 copies · chains A, D, B, C

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

Pockets

8 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	104	0.61	0.87	21	BTN
2	108	0.58	0.85	26	BTN
3	153	0.58	0.83	27	empty
4	115	0.57	0.84	26	BTN
5	228	0.57	0.79	30	empty

Interfaces

6 interfaces between chains.

C–D · 1639 Å² buried · 27 hydrogen bonds · protein-protein
A–B · 1626 Å² buried · 28 hydrogen bonds · protein-protein
A–D · 543 Å² buried · 2 hydrogen bonds · protein-protein
B–C · 536 Å² buried · 2 hydrogen bonds · protein-protein
B–D · 213 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

4YVB · Structure of D128N 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 4YVB · PDBe 4YVB · UniProt P22629

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