MolNFT v1 · #123494 · protein + DNA

Antphd with 15BP DNA duplex R-monothioated at cytidine-8

5JLW · Homeotic protein antennapedia: “Antphd with 15BP DNA duplex R-monothioated at cytidine-8”. X-ray diffraction, 1 ligand (NI), 5 pockets (best druggability 0.63). MolNFT v1 #123494 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 5JLW
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*(C7R)…
UniProt: P02833
Ligands: NI
Pockets: 5 · best druggability 0.63

Structure

x-ray diffraction · 3 distinct chains · 70% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Homeotic protein antennapedia	protein	57	70% helix, 0% strand	P02833
B, E	DNA (5'-D(APGPAPAPAPGPCP(C7R) PAPTPTPAPGPAP*G)-3')	dna	15	—	—
C, F	DNA (5'-D(TPCPTPCPTPAPAPTPGPGPCPTPTPTP*C)- 3')	dna	15	—	—

Ligands and binding sites

NI · Nickel (II) ion · metal · 6 copies · chains A, D, B, C, E
MPD · (4S)-2-methyl-2,4-pentanediol · additive · 3 copies · chains F, D, E

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

Pockets

5 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	59	0.63	0.93	21	empty
2	244	0.54	0.77	28	empty
3	154	0.49	0.78	19	empty
4	70	0.39	0.79	15	empty
5	52	0.30	0.77	12	empty

Interfaces

7 interfaces between chains.

E–F · 634 Å² buried · 53 hydrogen bonds · nucleic-nucleic
B–C · 633 Å² buried · 59 hydrogen bonds · nucleic-nucleic
A–B · 539 Å² buried · 10 hydrogen bonds · protein-nucleic
A–D · 518 Å² buried · 9 hydrogen bonds · protein-protein
D–E · 493 Å² buried · 9 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 2 modified (nucleotide modification).

Compared structures

5JLW · AntpHD with 15bp DNA duplex R-monothioated at Cytidine-8 · 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 5JLW · PDBe 5JLW · UniProt P02833

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