MolNFT v1 · #140804 · protein

Myxococcus xanthus mgla in GDP bound conformation

5YMX: “Myxococcus xanthus mgla in GDP bound conformation”. X-ray diffraction, 1 ligand (GDP). MolNFT v1 #140804 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5YMX
Type: protein
Length: 397 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
UniProt: Q1DB04
Ligands: GDP

Structure

x-ray diffraction · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	—	protein	202	—	Q1DB04
B	—	protein	195	—	Q1DB04

Ligands and binding sites

GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
IMD · Imidazole · additive · 2 copies · chains A, B
EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A

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

Compared structures

5YMX · Myxococcus xanthus MglA in GDP bound conformation · the same entry in another collection · chain A against A, TM-score 1.00
Q1DB04 · AlphaFold monomer V2.0 prediction for mutual gliding-motility protein mgla (Q1DB04) · a predicted model of the same protein · chain B against A, TM-score 0.92

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 Q1DB04
Elsewhere: RCSB PDB 5YMX · PDBe 5YMX · UniProt Q1DB04

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