MolNFT v1 · #126794 · protein

Crystal structure of tdp-43 N-terminal domain at 2.1 a resolution

5MDI · Tar DNA-binding protein 43: “Crystal structure of tdp-43 N-terminal domain at 2.1 a resolution”. X-ray diffraction, 2 pockets (best druggability 0.35). MolNFT v1 #126794 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5MDI
Type: protein
Length: 157 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tar DNA-binding protein 43
UniProt: K7EJM5
Pockets: 2 · best druggability 0.35

Structure

x-ray diffraction · 2 distinct chains · 6% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tar DNA-binding protein 43	protein	78	6% helix, 38% strand	K7EJM5
B	Tar DNA-binding protein 43	protein	79	6% helix, 38% strand	K7EJM5

Ligands and binding sites

ACT · Acetate ion · additive · chains B

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	60	0.35	0.78	20	empty
2	94	0.32	0.73	20	empty

Interfaces

1 interface between chains.

A–B · 696 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (nonstandard).

Compared structures

5MDI · Crystal structure of TDP-43 N-terminal domain at 2.1 A resolution · the same entry in another collection · 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 K7EJM5
Elsewhere: RCSB PDB 5MDI · PDBe 5MDI · UniProt K7EJM5

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