MolNFT v1 · #144054 · protein

Human parp-1 bound to NAD+ analog benzamide adenine dinucleotide (bad)

6BHV · Poly [ADP-ribose] polymerase 1: “Human parp-1 bound to NAD+ analog benzamide adenine dinucleotide (bad)”. X-ray diffraction, 1 ligand (DQV), 6 pockets (best druggability 0.79). MolNFT v1 #144054 on GenesisL1: 3D structure, binding…

PDB: 6BHV
Type: protein
Length: 939 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Poly [ADP-ribose] polymerase 1
EC: 2.4.2.30
UniProt: P09874
Ligands: DQV
Pockets: 6 · best druggability 0.79

Structure

x-ray diffraction · 4 distinct chains · 27% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30)	protein	238	27% helix, 35% strand	P09874
B	Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30)	protein	237	27% helix, 35% strand	P09874
C	Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30)	protein	226	27% helix, 37% strand	P09874
D	Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30)	protein	238	27% helix, 35% strand	P09874

Ligands and binding sites

DQV · [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl [(2R,3S,4R,5S)-5-(3-carbamoylphenyl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name) · ligand · 4 copies · chains A, B, C, D

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

Pockets

6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1108	0.79	0.80	88	DQV
2	917	0.78	0.81	96	DQV
3	471	0.73	0.83	53	empty
4	675	0.69	0.77	56	empty
5	275	0.56	0.77	30	empty

Interfaces

6 interfaces between chains.

C–D · 1022 Å² buried · 7 hydrogen bonds · protein-protein
A–B · 756 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 668 Å² buried · 10 hydrogen bonds · protein-protein
A–D · 248 Å² buried · 1 hydrogen bond · protein-protein
B–D · 233 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

6BHV · Human PARP-1 bound to NAD+ analog benzamide adenine dinucleotide (BAD) · 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 P09874
Elsewhere: RCSB PDB 6BHV · PDBe 6BHV · UniProt P09874

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