MolNFT v1 · #109967 · protein + DNA

Antphd with 15BP DNA duplex

4XID · Homeotic protein antennapedia: “Antphd with 15BP DNA duplex”. X-ray diffraction, 1 ligand (NI), 4 pockets (best druggability 0.61). MolNFT v1 #109967 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4XID
Type: protein + DNA
Length: 174 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Homeotic protein antennapedia; DNA (5'-D(*AP*GP*AP*AP*AP*GP*CP*CP*AP*TP*TP*AP*GP*AP*G)…
UniProt: P02833
Ligands: NI
Pockets: 4 · best druggability 0.61

Structure

x-ray diffraction · 4 distinct chains · 70% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Homeotic protein antennapedia	protein	58	67% helix, 0% strand	P02833
B, E	DNA (5'-D(APGPAPAPAPGPCPCPAPTPTPAPGPAP*G)- 3')	dna	15	—	—
C, F	DNA (5'-D(TPCPTPCPTPAPAPTPGPGPCPTPTPTP*C)- 3')	dna	15	—	—
D	Homeotic protein antennapedia	protein	56	73% helix, 0% strand	P02833

Ligands and binding sites

NI · Nickel (II) ion · metal · 3 copies · chains B, D, E
MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A, C, D, E, F

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

Pockets

4 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	528	0.61	0.74	47	MPD
2	209	0.53	0.78	24	empty
3	92	0.48	0.82	14	empty
4	70	0.44	0.82	12	empty

Interfaces

7 interfaces between chains.

A–B · 653 Å² buried · 14 hydrogen bonds · protein-nucleic
B–C · 649 Å² buried · 67 hydrogen bonds · nucleic-nucleic
E–F · 632 Å² buried · 64 hydrogen bonds · nucleic-nucleic
D–E · 549 Å² buried · 13 hydrogen bonds · protein-nucleic
A–C · 477 Å² buried · 9 hydrogen bonds · protein-nucleic

Compared structures

4XID · AntpHD with 15bp DNA duplex · the same entry in another collection · chain F against F, TM-score 1.00
P02833 · AlphaFold monomer V2.0 prediction for homeotic protein antennapedia (P02833) · a predicted model of the same protein · chain D 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 P02833
Elsewhere: RCSB PDB 4XID · PDBe 4XID · UniProt P02833

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.