MolNFT v1 · #128105 · protein

Crystal structure of the parp domain of arabidopsis radical-induced cell DEATH1

5NGO · Inactive poly [ADP-ribose] polymerase RCD1: “Crystal structure of the parp domain of arabidopsis radical-induced cell DEATH1”. X-ray diffraction, 17 pockets (best druggability 0.84). MolNFT v1 #128105 on GenesisL1: 3D structure…

PDB: 5NGO
Type: protein
Length: 1,361 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Inactive poly [ADP-ribose] polymerase RCD1
UniProt: Q8RY59
Pockets: 17 · best druggability 0.84

Structure

x-ray diffraction · 7 distinct chains · 33% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Inactive poly [ADP-ribose] polymerase RCD1	protein	178	29% helix, 28% strand	Q8RY59
B	Inactive poly [ADP-ribose] polymerase RCD1	protein	167	35% helix, 29% strand	Q8RY59
E	Inactive poly [ADP-ribose] polymerase RCD1	protein	174	28% helix, 29% strand	Q8RY59
G, D	Inactive poly [ADP-ribose] polymerase RCD1	protein	177	29% helix, 28% strand	Q8RY59
F	Inactive poly [ADP-ribose] polymerase RCD1	protein	163	36% helix, 26% strand	Q8RY59
H	Inactive poly [ADP-ribose] polymerase RCD1	protein	162	36% helix, 27% strand	Q8RY59
C	Inactive poly [ADP-ribose] polymerase RCD1	protein	163	36% helix, 29% strand	Q8RY59

Pockets

17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	342	0.84	0.93	38	empty
2	100	0.69	0.93	25	empty
3	111	0.68	0.91	24	empty
4	133	0.67	0.89	30	empty
5	319	0.65	0.81	43	empty

Interfaces

10 interfaces between chains.

A–B · 1271 Å² buried · 2 hydrogen bonds · protein-protein
G–H · 1212 Å² buried · 3 hydrogen bonds · protein-protein
D–C · 1203 Å² buried · 2 hydrogen bonds · protein-protein
E–F · 1157 Å² buried · 2 hydrogen bonds · protein-protein
B–C · 1041 Å² buried · 18 hydrogen bonds · protein-protein

Compared structures

5NGO · Crystal structure of the PARP domain of Arabidopsis RADICAL-INDUCED CELL DEATH1 · the same entry in another collection · chain C against C, TM-score 1.00
Q8RY59 · AlphaFold monomer V2.0 prediction for inactive poly [ADP-ribose] polymerase RCD1 (Q8RY59) · a predicted model of the same protein · chain G 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 Q8RY59
Elsewhere: RCSB PDB 5NGO · PDBe 5NGO · UniProt Q8RY59

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