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Crystal structure of putative ADP ribose pyrophosphatase

Analyse Crystal structure of putative ADP ribose pyrophosphatase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1VIU
Type: protein
Length: 715 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ADP-ribose pyrophosphatase
UniProt: P37128
Pockets: 5 · best druggability 0.67

Structure

x-ray diffraction · 4 distinct chains · 22% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	ADP-ribose pyrophosphatase	protein	180	21% helix, 42% strand	P37128
B	ADP-ribose pyrophosphatase	protein	181	22% helix, 44% strand	P37128
C	ADP-ribose pyrophosphatase	protein	175	23% helix, 43% strand	P37128
D	ADP-ribose pyrophosphatase	protein	179	22% helix, 45% strand	P37128

Pockets

5 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	723	0.67	0.75	71	empty
2	347	0.66	0.81	48	empty
3	332	0.64	0.80	48	empty
4	310	0.63	0.80	50	empty
5	265	0.60	0.79	40	empty

Interfaces

4 interfaces between chains.

C–D · 2545 Å² buried · 30 hydrogen bonds · protein-protein
A–B · 2523 Å² buried · 33 hydrogen bonds · protein-protein
A–D · 253 Å² buried · 3 hydrogen bonds · protein-protein
B–D · 61 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 modified (engineered).

Compared structures

1VIU · Crystal structure of putative ADP ribose pyrophosphatase · the same entry in another collection · chain D against D, TM-score 1.00
P37128 · AlphaFold monomer V2.0 prediction for GDP-mannose pyrophosphatase (P37128) · a predicted model of the same protein · chain B against A, TM-score 0.99

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 P37128
Elsewhere: RCSB PDB 1VIU · PDBe 1VIU · UniProt P37128

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