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Crystal structure of matp-mats

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

PDB: 3VEB
Type: protein + DNA
Length: 328 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Macrodomain ter protein; 5'-D(*TP*CP*GP*TP*GP*AP*CP*AP*TP*TP*GP*TP*CP*AP*CP*G)-3'…
UniProt: Q8ZG78
Ligands: CA
Pockets: 7 · best druggability 0.74

Structure

x-ray diffraction · 4 distinct chains · 68% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Macrodomain ter protein	protein	150	64% helix, 4% strand	Q8ZG78
N	5'-D(TPCPGPTPGPAPCPAPTPTPGPTPCPAPCPG)-3'	dna	16	—	—
M	5'-D(APCPGPTPGPAPCPAPAPTPGPTPCPAPCPG)-3'	dna	16	—	—
A	Macrodomain ter protein	protein	146	73% helix, 4% strand	Q8ZG78

Ligands and binding sites

CA · Calcium ion · metal · 3 copies · chains N, M

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

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	228	0.74	0.89	27	empty
2	283	0.68	0.84	33	empty
3	257	0.47	0.74	25	empty
4	116	0.45	0.78	21	empty
5	76	0.35	0.76	15	empty

Interfaces

6 interfaces between chains.

B–A · 2021 Å² buried · 18 hydrogen bonds · protein-protein
N–A · 720 Å² buried · 20 hydrogen bonds · protein-nucleic
N–M · 701 Å² buried · 84 hydrogen bonds · nucleic-nucleic
B–M · 687 Å² buried · 11 hydrogen bonds · protein-nucleic
M–A · 633 Å² buried · 13 hydrogen bonds · protein-nucleic

Compared structures

3VEB · Crystal Structure of Matp-matS · 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 A 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 3VEB · PDBe 3VEB · UniProt Q8ZG78

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