MolNFT v1 · #79311 · protein

Structure of apo shwanavidin (P21 form)

3SZI · AVIDIN/STREPTAVIDIN: “Structure of apo shwanavidin (P21 form)”. X-ray diffraction, 20 pockets (best druggability 0.80). MolNFT v1 #79311 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3SZI
Type: protein
Length: 1,411 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: AVIDIN/STREPTAVIDIN
UniProt: Q12QS6
Pockets: 20 · best druggability 0.80

Structure

x-ray diffraction · 9 distinct chains · 3% helix, 62% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	AVIDIN/STREPTAVIDIN	protein	117	3% helix, 62% strand	Q12QS6
B	AVIDIN/STREPTAVIDIN	protein	113	3% helix, 66% strand	Q12QS6
C, H, I	AVIDIN/STREPTAVIDIN	protein	117	3% helix, 62% strand	Q12QS6
D	AVIDIN/STREPTAVIDIN	protein	120	3% helix, 63% strand	Q12QS6
E	AVIDIN/STREPTAVIDIN	protein	118	5% helix, 58% strand	Q12QS6
F	AVIDIN/STREPTAVIDIN	protein	117	3% helix, 62% strand	Q12QS6
G, J	AVIDIN/STREPTAVIDIN	protein	119	3% helix, 61% strand	Q12QS6
K	AVIDIN/STREPTAVIDIN	protein	117	3% helix, 63% strand	Q12QS6
L	AVIDIN/STREPTAVIDIN	protein	120	3% helix, 62% strand	Q12QS6

Ligands and binding sites

FMT · Formic acid · additive · 6 copies · chains D, H, I, K, J

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1120	0.80	0.81	124	empty
2	252	0.69	0.85	43	empty
3	250	0.68	0.85	41	empty
4	244	0.68	0.84	41	empty
5	108	0.60	0.86	21	FMT

Interfaces

38 interfaces between chains.

A–B · 1740 Å² buried · 25 hydrogen bonds · protein-protein
G–H · 1728 Å² buried · 23 hydrogen bonds · protein-protein
E–F · 1725 Å² buried · 27 hydrogen bonds · protein-protein
C–D · 1717 Å² buried · 27 hydrogen bonds · protein-protein
I–J · 1692 Å² buried · 24 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide (disulfide).

Compared structures

3SZI · Structure of apo shwanavidin (P21 form) · 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 Q12QS6
Elsewhere: RCSB PDB 3SZI · PDBe 3SZI · UniProt Q12QS6

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