MolNFT v1 · #155900 · protein + DNA

Asfv PA104R in complex with double-strand DNA

6LMJ: “Asfv PA104R in complex with double-strand DNA”. X-ray diffraction, 2 pockets (best druggability 0.69). MolNFT v1 #155900 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6LMJ
Type: protein + DNA
Length: 235 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: A104R; DNA (5'- D(*TP*GP*CP*TP*TP*AP*TP*CP*AP*AP*TP*TP*TP*GP*TP*TP*GP*CP*A)-3')
UniProt: A0A0A1E0L7
Pockets: 2 · best druggability 0.69

Structure

x-ray diffraction · 3 distinct chains · 38% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	A104R	protein	99	38% helix, 29% strand	A0A0A1E0L7
B	A104R	protein	98	38% helix, 32% strand	A0A0A1E0L7
C, D	DNA (5'- D(TPGPCPTPTPAPTPCPAPAPTPTPTPGPTPTPGPCP*A)-3')	dna	19	—	—

Pockets

2 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	761	0.69	0.77	61	empty
2	178	0.50	0.78	18	empty

Interfaces

6 interfaces between chains.

A–B · 2372 Å² buried · 12 hydrogen bonds · protein-protein
C–D · 768 Å² buried · 69 hydrogen bonds · nucleic-nucleic
B–D · 167 Å² buried · 2 hydrogen bonds · protein-nucleic
A–D · 151 Å² buried · 2 hydrogen bonds · protein-nucleic
B–C · 117 Å² buried · 2 hydrogen bonds · protein-nucleic

Compared structures

6LMJ · ASFV pA104R in complex with double-strand DNA · the same entry in another collection · chain A against A, TM-score 1.00

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 A0A0A1E0L7
Elsewhere: RCSB PDB 6LMJ · PDBe 6LMJ · UniProt A0A0A1E0L7

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