MolNFT v1 · #91744 · protein

Espg-RAB1-ARF6 complex

4FME · Espg protein: “Espg-RAB1-ARF6 complex”. X-ray diffraction, 4 ligands (AF3, GDP, GTP), 20 pockets (best druggability 0.81). MolNFT v1 #91744 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4FME
Type: protein
Length: 1,364 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Espg protein; RAS-related protein rab-1A; ADP-ribosylation factor 6
UniProt: Q5WMC0, P62820, P62330
Ligands: AF3, GDP, GTP, MG
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 3 distinct chains · 32% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Espg protein	protein	351	32% helix, 24% strand	Q5WMC0
B, E	RAS-related protein rab-1A	protein	171	33% helix, 21% strand	P62820
C, F	ADP-ribosylation factor 6	protein	160	31% helix, 27% strand	P62330

Ligands and binding sites

AF3 · Aluminum fluoride · ligand · 2 copies · chains A, B, D, E
GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B, D, E
GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains C, F
MG · Magnesium ion · metal · 4 copies · chains B, C, E, F

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

Pockets

20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	516	0.81	0.88	68	AF3, GDP, MG
2	579	0.80	0.86	69	AF3, GDP, MG
3	999	0.76	0.78	84	empty
4	444	0.63	0.77	48	GTP, MG
5	372	0.60	0.77	37	GTP, MG

Interfaces

8 interfaces between chains.

A–B · 1509 Å² buried · 21 hydrogen bonds · protein-protein
D–E · 1481 Å² buried · 21 hydrogen bonds · protein-protein
A–C · 565 Å² buried · 7 hydrogen bonds · protein-protein
D–F · 564 Å² buried · 7 hydrogen bonds · protein-protein
C–F · 264 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

4FME · EspG-Rab1-Arf6 complex · the same entry in another collection · chain F against F, TM-score 1.00
P62330 · AlphaFold monomer V2.0 prediction for ADP-ribosylation factor 6 (P62330) · a predicted model of the same protein · chain F against A, TM-score 0.98
P62820 · AlphaFold monomer V2.0 prediction for RAS-related protein rab-1A (P62820) · a predicted model of the same protein · chain B 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 Q5WMC0
Every structure of UniProt P62820
Every structure of UniProt P62330
Elsewhere: RCSB PDB 4FME · PDBe 4FME · UniProt Q5WMC0 · UniProt P62820 · UniProt P62330

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