MolNFT v1 · #164639 · protein

Crystal structure of human tdp-43 N-terminal domain at 2.55 a resolution

6T4B · Tar DNA-binding protein 43: “Crystal structure of human tdp-43 N-terminal domain at 2.55 a resolution”. X-ray diffraction, 1 ligand (SO4), 5 pockets (best druggability 0.41). MolNFT v1 #164639 on GenesisL1: 3D structure, binding…

PDB: 6T4B
Type: protein
Length: 390 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tar DNA-binding protein 43
UniProt: Q13148
Ligands: SO4
Pockets: 5 · best druggability 0.41

Structure

x-ray diffraction · 3 distinct chains · 9% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E, I	Tar DNA-binding protein 43	protein	78	9% helix, 38% strand	Q13148
C	Tar DNA-binding protein 43	protein	79	9% helix, 38% strand	Q13148
G	Tar DNA-binding protein 43	protein	77	9% helix, 39% strand	Q13148

Ligands and binding sites

SO4 · Sulfate ion · ion · 5 copies · chains A, I, C, E, G

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

Pockets

5 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	72	0.41	0.80	20	SO4
2	82	0.32	0.73	19	empty
3	97	0.31	0.72	19	empty
4	61	0.27	0.73	14	empty
5	63	0.27	0.73	16	empty

Interfaces

4 interfaces between chains.

C–E · 760 Å² buried · 13 hydrogen bonds · protein-protein
A–C · 723 Å² buried · 12 hydrogen bonds · protein-protein
E–G · 702 Å² buried · 13 hydrogen bonds · protein-protein
A–I · 700 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

6T4B · Crystal structure of human tdp-43 N-terminal domain at 2.55 a resolution · the same entry in another collection · chain I against I, TM-score 1.00
Q13148 · AlphaFold monomer V2.0 prediction for tar DNA-binding protein 43 (Q13148) · a predicted model of the same protein · chain G against A, TM-score 0.96

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 Q13148
Elsewhere: RCSB PDB 6T4B · PDBe 6T4B · UniProt Q13148

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