MolNFT v1 · #13549 · protein

Complex of GGA3-vhs domain and ci-mpr C-terminal phosphopeptide

1LF8 · ADP-ribosylation factor binding protein GGA3: “Complex of GGA3-vhs domain and ci-mpr C-terminal phosphopeptide”. X-ray diffraction, 5 pockets (best druggability 0.78). MolNFT v1 #13549 on GenesisL1: 3D structure, binding sites and…

PDB: 1LF8
Type: protein
Length: 650 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ADP-ribosylation factor binding protein GGA3; Cation-independent mannose-6-phosphate…
UniProt: Q9NZ52, P11717
Pockets: 5 · best druggability 0.78

Structure

x-ray diffraction · 4 distinct chains · 68% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	ADP-ribosylation factor binding protein GGA3	protein	151	68% helix, 1% strand	Q9NZ52
B, D	ADP-ribosylation factor binding protein GGA3	protein	159	70% helix, 1% strand	Q9NZ52
C	ADP-ribosylation factor binding protein GGA3	protein	149	68% helix, 0% strand	Q9NZ52
E, F, G, H	Cation-independent mannose-6-phosphate receptor	protein	8	0% helix, 0% strand	P11717

Pockets

5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1093	0.78	0.79	74	empty
2	1037	0.76	0.79	78	empty
3	227	0.67	0.84	20	empty
4	127	0.59	0.85	22	empty
5	151	0.50	0.78	16	empty

Interfaces

9 interfaces between chains.

A–D · 802 Å² buried · 10 hydrogen bonds · protein-protein
B–C · 800 Å² buried · 12 hydrogen bonds · protein-protein
B–F · 603 Å² buried · 8 hydrogen bonds · protein-protein
A–E · 598 Å² buried · 10 hydrogen bonds · protein-protein
C–G · 596 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (phosphorylation).

Compared structures

1LF8 · Complex of GGA3-VHS Domain and CI-MPR C-terminal Phosphopeptide · the same entry in another collection · chain H against H, TM-score 1.00
Q9NZ52 · AlphaFold monomer V2.0 prediction for ADP-ribosylation factor-binding protein GGA3… · a predicted model of the same protein · chain A against A, TM-score 0.97

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 Q9NZ52
Every structure of UniProt P11717
Elsewhere: RCSB PDB 1LF8 · PDBe 1LF8 · UniProt Q9NZ52 · UniProt P11717

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