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Mtaqi with baz

Analyse Mtaqi with baz in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2JG3
Type: protein + DNA
Length: 822 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Modification methylase taqi; 5'-D(*GP*TP*TP*CP*GP*AP*TP*GP*TP*CP)-3'…
EC: 2.1.1.72
UniProt: P14385
Ligands: BA2, K
Pockets: 9 · best druggability 0.56

Structure

x-ray diffraction · 3 distinct chains · 30% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Modification methylase taqi (EC 2.1.1.72)	protein	391	30% helix, 28% strand	P14385
B, E	5'-D(GPTPTPCPGPAPTPGPTPCP)-3'	dna	10	—	—
C, F	5'-D(GPAPCPAPTPCPGP6MAPAPCP)-3'	dna	10	—	—

Ligands and binding sites

BA2 · 5'-deoxy-5'-(ethylamino)-8-{[4-({5-[(3as,4s,6ar)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoyl}amino)butyl]amino}adenosine · ligand · 2 copies · chains A, B, D, E
K · Potassium ion · metal · 2 copies · chains A, B, D, E
GOL · Glycerol · additive · 2 copies · chains A, B, C

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

Pockets

9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	240	0.56	0.78	36	empty
2	204	0.56	0.80	29	empty
3	312	0.54	0.75	42	empty
4	135	0.45	0.76	25	BA2, GOL, K
5	132	0.43	0.76	27	K, BA2

Interfaces

7 interfaces between chains.

D–E · 1110 Å² buried · 15 hydrogen bonds · protein-nucleic
A–B · 1085 Å² buried · 18 hydrogen bonds · protein-nucleic
A–C · 968 Å² buried · 18 hydrogen bonds · protein-nucleic
D–F · 964 Å² buried · 16 hydrogen bonds · protein-nucleic
B–C · 506 Å² buried · 37 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 2 modified (nucleotide modification).

Compared structures

2JG3 · MtaqI with BAZ · the same entry in another collection · chain C against C, TM-score 1.00
P14385 · AlphaFold monomer V2.0 prediction for modification methylase taqi (P14385) · a predicted model of the same protein · 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 P14385
Elsewhere: RCSB PDB 2JG3 · PDBe 2JG3 · UniProt P14385

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