MolNFT v1 · #55597 · protein + DNA

Structure of the AVRBS3-DNA complex provides new insights into the initial thymine-recognition mechanism

2YPF: “Structure of the AVRBS3-DNA complex provides new insights into the initial thymine-recognition mechanism”. X-ray diffraction, 4 pockets (best druggability 0.79). MolNFT v1 #55597 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 2YPF
Type: protein + DNA
Length: 718 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: AVRBS3; 5'-D(*TP*TP*TP*AP*TP*AP*TP*AP*AP*AP*CP*CP*TP*AP *AP*CP*CP*CP*TP*CP*TP*AP)-3'…
Pockets: 4 · best druggability 0.79

Structure

x-ray diffraction · 3 distinct chains · 59% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	AVRBS3	protein	675	59% helix, 0% strand	—
B	5'-D(TPTPTPAPTPAPTPAPAPAPCPCPTPAP APCPCPCPTPCPTPAP)-3'	dna	22	—	—
C	5'-D(TPAPGPAPGPGPGPTPTPAPGPGPTPTP TPAPTPAPTPAP*AP)-3'	dna	21	—	—

Pockets

4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1067	0.79	0.81	102	empty
2	447	0.62	0.76	47	empty
3	57	0.51	0.86	18	empty
4	283	0.49	0.74	39	empty

Interfaces

3 interfaces between chains.

A–B · 2430 Å² buried · 24 hydrogen bonds · protein-nucleic
B–C · 932 Å² buried · 102 hydrogen bonds · nucleic-nucleic
A–C · 289 Å² buried · 1 hydrogen bond · protein-nucleic

Compared structures

2YPF · Structure of the AvrBs3-DNA complex provides new insights into the initial… · 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
Elsewhere: RCSB PDB 2YPF · PDBe 2YPF

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