MolNFT v1 · #144547 · protein + DNA

DNA substrate selection by APOBEC3G

6BWY · DNA (30-mer): “DNA substrate selection by APOBEC3G”. X-ray diffraction, 2 ligands (ZN, PO4), 20 pockets (best druggability 0.72). MolNFT v1 #144547 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6BWY
Type: protein + DNA
Length: 1,410 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (30-mer); Protection of telomeres protein 1, DNA dc-&gt
EC: 3.5.4.-
UniProt: O13988, Q9HC16
Ligands: ZN, PO4
Pockets: 20 · best druggability 0.72

Structure

x-ray diffraction · 3 distinct chains · 25% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
I, C, D, F	DNA (30-mer)	dna	7	—	—
A	Protection of telomeres protein 1, DNA dc-&gt (EC 3.5.4.-)	protein	344	24% helix, 32% strand	O13988, Q9HC16
B, E, G	Protection of telomeres protein 1, DNA dc-&gt (EC 3.5.4.-)	protein	346	26% helix, 32% strand	O13988, Q9HC16

Ligands and binding sites

ZN · Zinc ion · metal · 4 copies · chains A, B, E, G
PO4 · Phosphate ion · ion · 15 copies · chains I, C, G, D, F, A, B, E

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

Pockets

20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	268	0.72	0.86	41	empty
2	833	0.69	0.75	67	empty
3	776	0.68	0.75	48	PO4
4	192	0.57	0.81	32	empty
5	258	0.52	0.75	33	empty

Interfaces

9 interfaces between chains.

A–B · 1248 Å² buried · 16 hydrogen bonds · protein-protein
E–G · 706 Å² buried · 11 hydrogen bonds · protein-protein
I–A · 681 Å² buried · 29 hydrogen bonds · protein-nucleic
F–E · 670 Å² buried · 27 hydrogen bonds · protein-nucleic
C–G · 659 Å² buried · 25 hydrogen bonds · protein-nucleic

Compared structures

6BWY · DNA substrate selection by APOBEC3G · the same entry in another collection · chain G against G, TM-score 1.00
Q9HC16 · AlphaFold monomer V2.0 prediction for DNA dc->du-editing enzyme apobec-3G (Q9HC16) · a predicted model of the same protein · chain A against A, TM-score 0.64

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 O13988
Every structure of UniProt Q9HC16
Elsewhere: RCSB PDB 6BWY · PDBe 6BWY · UniProt O13988 · UniProt Q9HC16

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