MolNFT v1 · #117688 · protein

Structural basis for specific recognition of ssdna by srbsdv P9-1 octamers

5EFT: “Structural basis for specific recognition of ssdna by srbsdv P9-1 octamers”. X-ray diffraction, 12 pockets (best druggability 0.71). MolNFT v1 #117688 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5EFT
Type: protein
Length: 1,084 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: P9-1
UniProt: B6SCH3
Pockets: 12 · best druggability 0.71

Structure

x-ray diffraction · 2 distinct chains · 39% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E, G	P9-1	protein	16	0% helix, 0% strand	B6SCH3
B, D, F, H	P9-1	protein	255	42% helix, 20% strand	B6SCH3

Pockets

12 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	788	0.71	0.77	62	empty
2	448	0.60	0.75	45	empty
3	51	0.45	0.85	16	empty
4	195	0.44	0.73	27	empty
5	118	0.41	0.75	19	empty

Interfaces

15 interfaces between chains.

D–H · 891 Å² buried · 9 hydrogen bonds · protein-protein
E–F · 774 Å² buried · 7 hydrogen bonds · protein-protein
C–D · 772 Å² buried · 7 hydrogen bonds · protein-protein
A–B · 772 Å² buried · 7 hydrogen bonds · protein-protein
G–H · 771 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

5EFT · Structural Basis for Specific Recognition of ssDNA by SRBSDV P9-1 Octamers · 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 B6SCH3
Elsewhere: RCSB PDB 5EFT · PDBe 5EFT · UniProt B6SCH3

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