MolNFT v1 · #141435 · protein + DNA

P204HINAB-dsdna complex structure

5Z7D · Interferon-activable protein 204: “P204HINAB-dsdna complex structure”. X-ray diffraction, 20 pockets (best druggability 0.76). MolNFT v1 #141435 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5Z7D
Type: protein + DNA
Length: 1,252 residues
Chains: 7
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Interferon-activable protein 204; DNA (5'- D(P*CP*CP*AP*TP*CP*AP*GP*AP*AP*AP*GP*AP*GP*AP*G…
UniProt: P0DOV2
Pockets: 20 · best druggability 0.76

Structure

x-ray diffraction · 5 distinct chains · 10% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Interferon-activable protein 204	protein	395	11% helix, 47% strand	P0DOV2
B	Interferon-activable protein 204	protein	397	11% helix, 46% strand	P0DOV2
C	Interferon-activable protein 204	protein	396	8% helix, 44% strand	P0DOV2
I, K	DNA (5'- D(PCPCPAPTPCPAPGPAPAPAPGPAPGPAPGPC)-3')	dna	16	—	—
J, L	DNA (5'- D(PCPCPAPTPCPAPGPAPAPAPGPAPGPAPGPC)-3')	dna	16	—	—

Pockets

20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	812	0.76	0.80	71	empty
2	827	0.73	0.78	98	empty
3	317	0.68	0.82	53	empty
4	652	0.67	0.76	45	empty
5	76	0.67	0.94	20	empty

Interfaces

15 interfaces between chains.

A–B · 942 Å² buried · 15 hydrogen bonds · protein-protein
B–C · 881 Å² buried · 7 hydrogen bonds · protein-protein
I–J · 740 Å² buried · 54 hydrogen bonds · nucleic-nucleic
K–L · 737 Å² buried · 64 hydrogen bonds · nucleic-nucleic
C–L · 286 Å² buried · 4 hydrogen bonds · protein-nucleic

Compared structures

5Z7D · p204HINab-dsDNA complex structure · the same entry in another collection · chain L against L, TM-score 1.00
P0DOV2 · AlphaFold monomer V2.0 prediction for interferon-activable protein 204 (P0DOV2) · a predicted model of the same protein · chain B against A, TM-score 0.98

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 P0DOV2
Elsewhere: RCSB PDB 5Z7D · PDBe 5Z7D · UniProt P0DOV2

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