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Crystal structure of matp-MATS23MER

Analyse Crystal structure of matp-MATS23MER in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3VEA
Type: protein + DNA
Length: 344 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Macrodomain ter protein; 5'-D(*AP*GP*TP*TP*CP*GP*TP*GP*AP*CP*AP*TP*TP*GP*TP*CP*AP*CP…
UniProt: Q8ZG78
Pockets: 7 · best druggability 0.71

Structure

x-ray diffraction · 3 distinct chains · 73% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B, A	Macrodomain ter protein	protein	149	73% helix, 6% strand	Q8ZG78
N	5'-D(APGPTPTPCPGPTPGPAPCPAPTPTPGPTPCPAPCP GPAPAPCP*T)-3'	dna	23	—	—
M	5'-D(APGPTPTPCPGPTPGPAPCPAPAPTPGPTPCPAPCP GPAPAPCP*T)-3'	dna	23	—	—

Pockets

7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	220	0.71	0.88	28	empty
2	229	0.70	0.87	28	empty
3	197	0.49	0.76	26	empty
4	140	0.47	0.78	20	empty
5	194	0.41	0.72	18	empty

Interfaces

6 interfaces between chains.

B–A · 2208 Å² buried · 16 hydrogen bonds · protein-protein
N–M · 1005 Å² buried · 92 hydrogen bonds · nucleic-nucleic
B–M · 723 Å² buried · 16 hydrogen bonds · protein-nucleic
N–A · 691 Å² buried · 15 hydrogen bonds · protein-nucleic
B–N · 638 Å² buried · 12 hydrogen bonds · protein-nucleic

Compared structures

3VEA · Crystal Structure of matP-matS23mer · the same entry in another collection · chain B against B, TM-score 1.00
Q8ZG78 · AlphaFold monomer V2.0 prediction for macrodomain ter protein (Q8ZG78) · a predicted model of the same protein · chain B against A, TM-score 0.90

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 Q8ZG78
Elsewhere: RCSB PDB 3VEA · PDBe 3VEA · UniProt Q8ZG78

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