MolNFT v1 · #124411 · protein + DNA

Crystal structure of APOBEC3A in complex with a single-stranded DNA

5KEG · DNA dc->du-editing enzyme apobec-3A: “Crystal structure of APOBEC3A in complex with a single-stranded DNA”. X-ray diffraction, 3 ligands (ZN, CA, CL). MolNFT v1 #124411 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5KEG
Type: protein + DNA
Length: 191 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA dc->du-editing enzyme apobec-3A; DNA (5'-D(*TP*TP*CP*TP*T)-3')
EC: 3.5.4.-
UniProt: P31941
Ligands: ZN, CA, CL

Structure

x-ray diffraction · 2 distinct chains · 38% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA dc->du-editing enzyme apobec-3A (EC 3.5.4.-)	protein	187	38% helix, 23% strand	P31941
B	DNA (5'-D(TPTPCPTP*T)-3')	dna	4	—	—

Ligands and binding sites

ZN · Zinc ion · metal · chains A
CA · Calcium ion · metal · chains A
CL · Chloride ion · ion · chains A, B

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

Interfaces

1 interface between chains.

A–B · 573 Å² buried · 16 hydrogen bonds · protein-nucleic

Compared structures

5KEG · Crystal structure of APOBEC3A in complex with a single-stranded DNA · the same entry in another collection · chain A against A, TM-score 1.00
P31941 · AlphaFold monomer V2.0 prediction for DNA dc->du-editing enzyme apobec-3A (P31941) · a predicted model of the same protein · chain A 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 P31941
Elsewhere: RCSB PDB 5KEG · PDBe 5KEG · UniProt P31941

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