MolNFT v1 · #175958 · protein

Cryo-EM structure of GMPPA/GMPPB complex bound to GTP (state I)

7D73 · Mannose-1-phosphate guanyltransferase alpha: “Cryo-EM structure of GMPPA/GMPPB complex bound to GTP (state I)”. Electron microscopy, 2 ligands (GTP, GDD), 20 pockets (best druggability 0.78). MolNFT v1 #175958 on GenesisL1: 3D…

PDB: 7D73
Type: protein
Length: 4,495 residues
Chains: 12
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Mannose-1-phosphate guanyltransferase alpha; Mannose-1-phosphate guanyltransferase beta
EC: 2.7.7.13
UniProt: Q96IJ6, Q9Y5P6
Ligands: GTP, GDD
Pockets: 20 · best druggability 0.78

Structure

electron microscopy · 4 distinct chains · 23% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Mannose-1-phosphate guanyltransferase alpha	protein	407	22% helix, 29% strand	Q96IJ6
B, C, D	Mannose-1-phosphate guanyltransferase alpha	protein	406	24% helix, 28% strand	Q96IJ6
E, G, I, J, K, L, H	Mannose-1-phosphate guanyltransferase beta (EC 2.7.7.13)	protein	360	22% helix, 27% strand	Q9Y5P6
F	Mannose-1-phosphate guanyltransferase beta (EC 2.7.7.13)	protein	350	24% helix, 28% strand	Q9Y5P6

Ligands and binding sites

GTP · Guanosine-5'-triphosphate · ligand · 10 copies · chains B, E, D, F, G, I, J, K, L, H
GDD · Guanosine-5'-diphosphate-alpha-D-mannose · ligand · 2 copies · chains A, C

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	145	0.78	0.95	33	empty
2	165	0.76	0.93	32	empty
3	625	0.73	0.80	61	GTP
4	629	0.73	0.80	59	GTP
5	331	0.72	0.85	40	GDD

Interfaces

21 interfaces between chains.

C–D · 987 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 987 Å² buried · 16 hydrogen bonds · protein-protein
C–I · 727 Å² buried · 14 hydrogen bonds · protein-protein
D–K · 713 Å² buried · 12 hydrogen bonds · protein-protein
B–F · 710 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 covalent, 2 disulfide (covalent ligand, disulfide).

Compared structures

7D73 · Cryo-EM structure of GMPPA/GMPPB complex bound to GTP (State I) · the same entry in another collection · chain H against H, 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 Q96IJ6
Every structure of UniProt Q9Y5P6
Elsewhere: RCSB PDB 7D73 · PDBe 7D73 · UniProt Q96IJ6 · UniProt Q9Y5P6

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