MolNFT v1 · #60365 · protein

Crystal structure of SEC4 in complex with rab-gdi

3CPH · Rab GDP-dissociation inhibitor: “Crystal structure of SEC4 in complex with rab-gdi”. X-ray diffraction, 2 ligands (GDP, MG), 14 pockets (best druggability 0.66). MolNFT v1 #60365 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 3CPH
Type: protein
Length: 1,052 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Rab GDP-dissociation inhibitor; RAS-related protein SEC4
UniProt: P39958, P07560
Ligands: GDP, MG
Pockets: 14 · best druggability 0.66

Structure

x-ray diffraction · 3 distinct chains · 34% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
G	Rab GDP-dissociation inhibitor	protein	441	36% helix, 24% strand	P39958
A	RAS-related protein SEC4	protein	175	35% helix, 23% strand	P07560
H	Rab GDP-dissociation inhibitor	protein	436	32% helix, 23% strand	P39958

Ligands and binding sites

GDP · Guanosine-5'-diphosphate · ligand · chains A
MG · Magnesium ion · metal · chains A

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

Pockets

14 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	359	0.66	0.81	50	MG, GDP
2	335	0.65	0.80	33	empty
3	430	0.63	0.77	53	empty
4	156	0.60	0.83	28	empty
5	387	0.58	0.75	40	empty

Interfaces

2 interfaces between chains.

G–A · 882 Å² buried · 17 hydrogen bonds · protein-protein
G–H · 553 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

3CPH · Crystal structure of Sec4 in complex with Rab-GDI · the same entry in another collection · chain G against G, TM-score 1.00
P39958 · AlphaFold monomer V2.0 prediction for rab GDP-dissociation inhibitor (P39958) · a predicted model of the same protein · chain H against A, TM-score 0.99
P07560 · AlphaFold monomer V2.0 prediction for RAS-related protein SEC4 (P07560) · a predicted model of the same protein · chain A against A, TM-score 0.92

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 P39958
Every structure of UniProt P07560
Elsewhere: RCSB PDB 3CPH · PDBe 3CPH · UniProt P39958 · UniProt P07560

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