MolNFT v1 · #91742 · protein

Espg-RAB1 complex

4FMC · RORF2: “Espg-RAB1 complex”. X-ray diffraction, 3 ligands (AF3, GDP, MG), 20 pockets (best druggability 0.83). MolNFT v1 #91742 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4FMC
Type: protein
Length: 1,464 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RORF2; RAS-related protein rab-1A
UniProt: O52121, P62820
Ligands: AF3, GDP, MG
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 5 distinct chains · 33% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RORF2	protein	351	33% helix, 25% strand	O52121
B, D	RAS-related protein rab-1A	protein	171	37% helix, 27% strand	P62820
C	RORF2	protein	350	33% helix, 25% strand	O52121
E	RORF2	protein	348	32% helix, 25% strand	O52121
F	RAS-related protein rab-1A	protein	73	23% helix, 5% 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, D

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

Pockets

20 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	939	0.83	0.84	100	AF3, GDP, MG
2	1117	0.83	0.84	98	PGE
3	406	0.79	0.88	60	AF3, GDP, MG
4	597	0.67	0.77	75	AF3, GDP, MG
5	631	0.66	0.76	38	empty

Interfaces

9 interfaces between chains.

C–D · 1503 Å² buried · 19 hydrogen bonds · protein-protein
A–B · 1474 Å² buried · 22 hydrogen bonds · protein-protein
E–F · 1196 Å² buried · 13 hydrogen bonds · protein-protein
A–C · 821 Å² buried · 8 hydrogen bonds · protein-protein
D–E · 317 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

4FMC · EspG-Rab1 complex · 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 O52121
Every structure of UniProt P62820
Elsewhere: RCSB PDB 4FMC · PDBe 4FMC · UniProt O52121 · UniProt P62820

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