MolNFT v1 · #72119 · protein

Mycoplasma genitalium MG289

3MYU · High affinity transport system protein P37: “Mycoplasma genitalium MG289”. X-ray diffraction, 1 ligand (VIB), 8 pockets (best druggability 0.73). MolNFT v1 #72119 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3MYU
Type: protein
Length: 667 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: High affinity transport system protein P37
UniProt: Q49410
Ligands: VIB
Pockets: 8 · best druggability 0.73

Structure

x-ray diffraction · 2 distinct chains · 41% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	High affinity transport system protein P37	protein	333	41% helix, 24% strand	Q49410
B	High affinity transport system protein P37	protein	334	41% helix, 24% strand	Q49410

Ligands and binding sites

VIB · 3-(4-amino-2-methyl-pyrimidin-5-ylmethyl)-5-(2-hydroxy-ethyl)-4-methyl-thiazol-3-ium · ligand · 2 copies · chains A, B
ACT · Acetate ion · additive · 2 copies · chains A, B

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

Pockets

8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	626	0.73	0.80	57	VIB
2	576	0.72	0.80	55	VIB
3	375	0.63	0.78	38	empty
4	261	0.60	0.80	36	empty
5	196	0.54	0.78	28	empty

Interfaces

1 interface between chains.

A–B · 1140 Å² buried · 17 hydrogen bonds · protein-protein

Compared structures

3MYU · Mycoplasma genitalium MG289 · the same entry in another collection · chain A against A, TM-score 1.00
Q49410 · AlphaFold monomer V2.0 prediction for high affinity transport system protein P37 (Q49410) · a predicted model of the same protein · chain B 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 Q49410
Elsewhere: RCSB PDB 3MYU · PDBe 3MYU · UniProt Q49410

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