MolNFT v1 · #91743 · protein

Espg-RAB1 complex structure at 3.05 a

4FMD · Espg protein: “Espg-RAB1 complex structure at 3.05 a”. X-ray diffraction, 3 ligands (AF3, GDP, MG), 15 pockets (best druggability 0.83). MolNFT v1 #91743 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4FMD
Type: protein
Length: 1,543 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Espg protein; RAS-related protein rab-1A
UniProt: Q5WMC0, P62820
Ligands: AF3, GDP, MG
Pockets: 15 · best druggability 0.83

Structure

x-ray diffraction · 4 distinct chains · 35% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Espg protein	protein	351	34% helix, 26% strand	Q5WMC0
B, D	RAS-related protein rab-1A	protein	171	36% helix, 28% strand	P62820
E	Espg protein	protein	350	34% helix, 25% strand	Q5WMC0
F	RAS-related protein rab-1A	protein	149	41% helix, 19% strand	P62820

Ligands and binding sites

AF3 · Aluminum fluoride · ligand · 3 copies · chains A, B, C, D, E, F
GDP · Guanosine-5'-diphosphate · ligand · 3 copies · chains A, B, C, D, E, F
MG · Magnesium ion · metal · 3 copies · chains B, D, F
PGE · Triethylene glycol · additive · chains A, B, C
PEG · Di(hydroxyethyl)ether · additive · chains E

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

Pockets

15 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1103	0.83	0.84	103	PGE
2	906	0.81	0.83	94	AF3, GDP, MG
3	408	0.79	0.88	60	AF3, GDP, MG
4	585	0.71	0.80	62	AF3, GDP, MG
5	406	0.61	0.77	59	empty

Interfaces

9 interfaces between chains.

A–B · 1539 Å² buried · 19 hydrogen bonds · protein-protein
C–D · 1505 Å² buried · 20 hydrogen bonds · protein-protein
E–F · 1327 Å² buried · 18 hydrogen bonds · protein-protein
A–C · 897 Å² buried · 9 hydrogen bonds · protein-protein
D–E · 232 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

4FMD · EspG-Rab1 complex structure at 3.05 A · the same entry in another collection · chain F against F, TM-score 1.00
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 0.98

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
Elsewhere: RCSB PDB 4FMD · PDBe 4FMD · UniProt Q5WMC0 · UniProt P62820

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