Research workbench

C-myc DNA unwinding element binding protein

Analyse C-myc DNA unwinding element binding protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2OKV
Type: protein
Length: 597 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Probable D-tyrosyl-TRNA(TYR) deacylase 1
EC: 3.1.-.-
UniProt: Q8TEA8
Ligands: MG
Pockets: 6 · best druggability 0.73

Structure

x-ray diffraction · 2 distinct chains · 27% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, D	Probable D-tyrosyl-TRNA(TYR) deacylase 1 (EC 3.1.-.-)	protein	149	28% helix, 38% strand	Q8TEA8
B	Probable D-tyrosyl-TRNA(TYR) deacylase 1 (EC 3.1.-.-)	protein	150	27% helix, 41% strand	Q8TEA8

Ligands and binding sites

MG · Magnesium ion · metal · 4 copies · chains A, B, C, D

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

Pockets

6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	623	0.73	0.80	71	empty
2	171	0.53	0.79	28	empty
3	147	0.51	0.79	25	empty
4	190	0.51	0.77	34	empty
5	138	0.49	0.79	29	empty

Interfaces

5 interfaces between chains.

C–D · 1699 Å² buried · 41 hydrogen bonds · protein-protein
A–B · 1688 Å² buried · 41 hydrogen bonds · protein-protein
B–C · 309 Å² buried · 5 hydrogen bonds · protein-protein
B–D · 146 Å² buried · 1 hydrogen bond · protein-protein
A–D · 118 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

2OKV · c-Myc DNA Unwinding Element Binding Protein · the same entry in another collection · chain D against D, TM-score 1.00
Q8TEA8 · AlphaFold monomer V2.0 prediction for D-aminoacyl-tRNA deacylase 1 (Q8TEA8) · a predicted model of the same protein · chain D 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 Q8TEA8
Elsewhere: RCSB PDB 2OKV · PDBe 2OKV · UniProt Q8TEA8

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