MolNFT v1 · #104291 · protein

Structure of exomer bound to ARF1.

4Q66 · CHS5P: “Structure of exomer bound to ARF1.”. X-ray diffraction, 2 ligands (GNP, MG), 20 pockets (best druggability 0.80). MolNFT v1 #104291 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4Q66
Type: protein
Length: 3,266 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: CHS5P; Protein BCH1; ADP-ribosylation factor 1
UniProt: W7PD87, Q05029, P11076
Ligands: GNP, MG
Pockets: 20 · best druggability 0.80

Structure

x-ray diffraction · 12 distinct chains · 46% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	CHS5P	protein	226	13% helix, 32% strand	W7PD87
J	CHS5P	protein	158	15% helix, 37% strand	W7PD87
G	CHS5P	protein	211	21% helix, 35% strand	W7PD87
D	CHS5P	protein	171	16% helix, 42% strand	W7PD87
K	Protein BCH1	protein	593	56% helix, 6% strand	Q05029
E	Protein BCH1	protein	557	60% helix, 5% strand	Q05029
B	Protein BCH1	protein	507	62% helix, 3% strand	Q05029
H	Protein BCH1	protein	338	68% helix, 1% strand	Q05029
F	ADP-ribosylation factor 1	protein	146	33% helix, 25% strand	P11076
L	ADP-ribosylation factor 1	protein	139	30% helix, 24% strand	P11076
C	ADP-ribosylation factor 1	protein	134	34% helix, 20% strand	P11076
I	ADP-ribosylation factor 1	protein	86	31% helix, 15% strand	P11076

Ligands and binding sites

GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 4 copies · chains F, L, A, C, G, I
MG · Magnesium ion · metal · 4 copies · chains F, L, C, I

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1046	0.80	0.82	101	GNP, MG
2	779	0.80	0.83	81	empty
3	1155	0.77	0.79	95	empty
4	353	0.76	0.86	52	empty
5	490	0.73	0.82	55	empty

Interfaces

22 interfaces between chains.

A–B · 1505 Å² buried · 18 hydrogen bonds · protein-protein
A–D · 1412 Å² buried · 20 hydrogen bonds · protein-protein
J–G · 1342 Å² buried · 19 hydrogen bonds · protein-protein
D–E · 1292 Å² buried · 14 hydrogen bonds · protein-protein
J–K · 1279 Å² buried · 23 hydrogen bonds · protein-protein

Compared structures

4Q66 · Structure of Exomer bound to Arf1. · the same entry in another collection · chain I against I, TM-score 1.00

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 W7PD87
Every structure of UniProt Q05029
Every structure of UniProt P11076
Elsewhere: RCSB PDB 4Q66 · PDBe 4Q66 · UniProt W7PD87 · UniProt Q05029 · UniProt P11076

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