MolNFT v1 · #138402 · protein

Crystal structure of DYNLT1/TCTEX-1 in complex with ARHGEF2

5WI4 · Dynein light chain tctex-type 1,RHO guanine nucleotide…: “Crystal structure of DYNLT1/TCTEX-1 in complex with ARHGEF2”. X-ray diffraction, 1 ligand (SO4), 3 pockets (best druggability 0.72). MolNFT v1 #138402 on GenesisL1: 3D…

PDB: 5WI4
Type: protein
Length: 375 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dynein light chain tctex-type 1,RHO guanine nucleotide exchange factor 2
UniProt: P51807, Q60875
Ligands: SO4
Pockets: 3 · best druggability 0.72

Structure

x-ray diffraction · 3 distinct chains · 32% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Dynein light chain tctex-type 1,RHO guanine nucleotide exchange factor 2	protein	125	32% helix, 36% strand	P51807, Q60875
B	Dynein light chain tctex-type 1,RHO guanine nucleotide exchange factor 2	protein	125	30% helix, 40% strand	P51807, Q60875
C	Dynein light chain tctex-type 1,RHO guanine nucleotide exchange factor 2	protein	125	33% helix, 32% strand	P51807, Q60875

Ligands and binding sites

SO4 · Sulfate ion · ion · 4 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	58	0.72	0.98	25	empty
2	179	0.47	0.76	21	empty
3	164	0.42	0.74	24	empty

Interfaces

2 interfaces between chains.

A–B · 1742 Å² buried · 30 hydrogen bonds · protein-protein
A–C · 148 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5WI4 · Crystal structure of DYNLT1/TCTEX-1 in complex with ARHGEF2 · the same entry in another collection · chain A against A, TM-score 1.00
P51807 · AlphaFold monomer V2.0 prediction for dynein light chain tctex-type 1 (P51807) · a predicted model of the same protein · chain A against A, TM-score 0.82
Q60875 · AlphaFold monomer V2.0 prediction for rho guanine nucleotide exchange factor 2 (Q60875) · a predicted model of the same protein · chain C against A, TM-score 0.35

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 P51807
Every structure of UniProt Q60875
Elsewhere: RCSB PDB 5WI4 · PDBe 5WI4 · UniProt P51807 · UniProt Q60875

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