MolNFT v1 · #128460 · protein

Structure of the arabidopsis thaliana topless N-terminal domain

5NQV · Protein topless: “Structure of the arabidopsis thaliana topless N-terminal domain”. X-ray diffraction, 10 pockets (best druggability 0.48). MolNFT v1 #128460 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5NQV
Type: protein
Length: 755 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein topless; Ear motif of IAA27
UniProt: Q94AI7
Pockets: 10 · best druggability 0.48

Structure

x-ray diffraction · 8 distinct chains · 68% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein topless	protein	180	72% helix, 0% strand	Q94AI7
B	Protein topless	protein	179	69% helix, 0% strand	Q94AI7
C	Protein topless	protein	190	68% helix, 0% strand	Q94AI7
D	Protein topless	protein	178	71% helix, 0% strand	Q94AI7
E	Ear motif of IAA27	protein	10	0% helix, 0% strand	—
F	Ear motif of IAA27	protein	9	0% helix, 0% strand	—
G	Ear motif of IAA27	protein	4	0% helix, 0% strand	—
H	Ear motif of IAA27	protein	5	0% helix, 0% strand	—

Ligands and binding sites

GOL · Glycerol · additive · 6 copies · chains B, A, C, E
TLA · L(+)-tartaric acid · additive · 4 copies · chains A, C, D

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

Pockets

10 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	156	0.48	0.77	19	empty
2	98	0.44	0.78	20	empty
3	76	0.33	0.75	12	empty
4	76	0.33	0.75	19	GOL
5	77	0.33	0.75	15	GOL

Interfaces

8 interfaces between chains.

A–C · 1404 Å² buried · 24 hydrogen bonds · protein-protein
B–D · 1303 Å² buried · 21 hydrogen bonds · protein-protein
B–F · 749 Å² buried · 5 hydrogen bonds · protein-protein
A–E · 710 Å² buried · 3 hydrogen bonds · protein-protein
C–D · 615 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

5NQV · Structure of the Arabidopsis Thaliana TOPLESS N-terminal domain · the same entry in another collection · chain H against H, TM-score 1.00
Q94AI7 · AlphaFold monomer V2.0 prediction for protein topless (Q94AI7) · a predicted model of the same protein · chain B 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 Q94AI7
Elsewhere: RCSB PDB 5NQV · PDBe 5NQV · UniProt Q94AI7

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