MolNFT v1 · #35572 · protein

ARA7-GDP/ATVPS9A

2EFC · Similarity to vacuolar protein sorting-associated protein…: “ARA7-GDP/ATVPS9A”. X-ray diffraction, 1 ligand (GDP), 8 pockets (best druggability 0.78). MolNFT v1 #35572 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2EFC
Type: protein
Length: 822 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Similarity to vacuolar protein sorting-associated protein VPS9; Small GTP-binding…
UniProt: Q9LT31, Q9SN68
Ligands: GDP
Pockets: 8 · best druggability 0.78

Structure

x-ray diffraction · 2 distinct chains · 58% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Similarity to vacuolar protein sorting-associated protein VPS9	protein	246	74% helix, 0% strand	Q9LT31
B, D	Small GTP-binding protein-like	protein	165	35% helix, 24% strand	Q9SN68

Ligands and binding sites

GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B, C, D

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

Pockets

8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	998	0.78	0.80	78	empty
2	232	0.52	0.76	34	empty
3	164	0.51	0.79	33	GDP
4	153	0.49	0.78	32	GDP
5	73	0.40	0.79	21	empty

Interfaces

5 interfaces between chains.

C–D · 1210 Å² buried · 22 hydrogen bonds · protein-protein
A–B · 1203 Å² buried · 20 hydrogen bonds · protein-protein
A–C · 554 Å² buried · 4 hydrogen bonds · protein-protein
B–C · 307 Å² buried · 3 hydrogen bonds · protein-protein
A–D · 282 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

2EFC · Ara7-GDP/AtVps9a · the same entry in another collection · chain A against A, TM-score 1.00
Q9LT31 · AlphaFold monomer V2.0 prediction for vacuolar protein sorting- associated protein 9A… · a predicted model of the same protein · chain A against A, TM-score 0.99
Q9SN68 · AlphaFold monomer V2.0 prediction for RAS-related protein RABF2B (Q9SN68) · a predicted model of the same protein · chain B against A, TM-score 0.93

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 Q9LT31
Every structure of UniProt Q9SN68
Elsewhere: RCSB PDB 2EFC · PDBe 2EFC · UniProt Q9LT31 · UniProt Q9SN68

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