MolNFT v1 · #187340 · protein + DNA

Structure of DRMAB:ADP:DNA complex

7S9W: “Structure of DRMAB:ADP:DNA complex”. Electron microscopy, 1 ligand (ADP), 20 pockets (best druggability 0.86). MolNFT v1 #187340 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7S9W
Type: protein + DNA
Length: 1,774 residues
Chains: 3
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Drma; Drmb; DNA (5'-D(P*TP*TP*TP*TP*TP*TP*T)-3')
Ligands: ADP
Pockets: 20 · best druggability 0.86

Structure

electron microscopy · 3 distinct chains · 31% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Drma	protein	1238	34% helix, 20% strand	—
B	Drmb	protein	529	25% helix, 26% strand	—
C	DNA (5'-D(PTPTPTPTPTPTP*T)-3')	dna	7	—	—

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · chains A

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

Pockets

20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	770	0.86	0.89	104	empty
2	773	0.85	0.88	80	empty
3	755	0.81	0.85	63	empty
4	671	0.79	0.84	68	empty
5	968	0.74	0.77	82	empty

Interfaces

3 interfaces between chains.

A–B · 3993 Å² buried · 28 hydrogen bonds · protein-protein
A–C · 847 Å² buried · 10 hydrogen bonds · protein-nucleic
B–C · 161 Å² buried · 1 hydrogen bond · protein-nucleic

Compared structures

7S9W · Structure of DrmAB:ADP:DNA complex · 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
Elsewhere: RCSB PDB 7S9W · PDBe 7S9W

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