MolNFT v1 · #141211 · protein + DNA

ATVAL1 B3 domain in complex with 15BP-DNA

5Z00 · DNA (5'-D(*AP*AP*TP*TP*CP*TP*GP*CP*AP*TP*GP*GP*AP*TP*T)- 3'): “ATVAL1 B3 domain in complex with 15BP-DNA”. X-ray diffraction, 7 pockets (best druggability 0.77). MolNFT v1 #141211 on GenesisL1: 3D structure, binding sites and…

PDB: 5Z00
Type: protein + DNA
Length: 534 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'-D(*AP*AP*TP*TP*CP*TP*GP*CP*AP*TP*GP*GP*AP*TP*T)- 3'); DNA…
UniProt: Q8W4L5
Pockets: 7 · best druggability 0.77

Structure

x-ray diffraction · 4 distinct chains · 16% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E, I	DNA (5'-D(APAPTPTPCPTPGPCPAPTPGPGPAPTP*T)- 3')	dna	15	—	—
B, J	DNA (5'-D(TPAPAPTPCPCPAPTPGPCPAPGPAPAP*T)- 3')	dna	15	—	—
C, G, K, M	B3 domain-containing transcription repressor VAL1	protein	111	16% helix, 45% strand	Q8W4L5
F	DNA (5'-D(TPAPAPTPCPCPAPTPGPCPAPGPAPAPTPT)- 3')	dna	15	—	—

Pockets

7 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	515	0.77	0.84	59	empty
2	816	0.73	0.78	63	empty
3	533	0.66	0.77	65	empty
4	105	0.46	0.79	22	empty
5	134	0.44	0.77	26	empty

Interfaces

15 interfaces between chains.

G–M · 778 Å² buried · 3 hydrogen bonds · protein-protein
C–K · 768 Å² buried · 10 hydrogen bonds · protein-protein
E–F · 687 Å² buried · 61 hydrogen bonds · nucleic-nucleic
I–J · 631 Å² buried · 61 hydrogen bonds · nucleic-nucleic
A–B · 629 Å² buried · 52 hydrogen bonds · nucleic-nucleic

Compared structures

5Z00 · AtVAL1 B3 domain in complex with 15bp-DNA · the same entry in another collection · chain M against M, TM-score 1.00
Q8W4L5 · AlphaFold monomer V2.0 prediction for B3 domain-containing transcription repressor VAL1… · a predicted model of the same protein · chain C against A, TM-score 0.97

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 Q8W4L5
Elsewhere: RCSB PDB 5Z00 · PDBe 5Z00 · UniProt Q8W4L5

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