MolNFT v1 · #108230 · protein

Crystal structure of BBS1N in complex with ARL6DN

4V0M · Arf-like small GTPase: “Crystal structure of BBS1N in complex with ARL6DN”. X-ray diffraction, 2 ligands (GTP, MG), 20 pockets (best druggability 0.82). MolNFT v1 #108230 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4V0M
Type: protein
Length: 1,934 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Arf-like small GTPase; Bardet-biedl syndrome 1 protein
UniProt: A8JF99, A8JEA1
Ligands: GTP, MG
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 6 distinct chains · 7% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, G	Arf-like small GTPase	protein	166	27% helix, 27% strand	A8JF99
B	Bardet-biedl syndrome 1 protein	protein	333	1% helix, 50% strand	A8JEA1
D	Bardet-biedl syndrome 1 protein	protein	303	1% helix, 53% strand	A8JEA1
E	Arf-like small GTPase	protein	166	29% helix, 25% strand	A8JF99
F	Bardet-biedl syndrome 1 protein	protein	309	1% helix, 53% strand	A8JEA1
H	Bardet-biedl syndrome 1 protein	protein	325	1% helix, 51% strand	A8JEA1

Ligands and binding sites

GTP · Guanosine-5'-triphosphate · ligand · 4 copies · chains A, C, E, G
MG · Magnesium ion · metal · 4 copies · chains A, C, E, G

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

Pockets

20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1077	0.82	0.83	114	GTP, MG
2	782	0.81	0.85	70	empty
3	929	0.79	0.81	71	empty
4	686	0.78	0.83	72	empty
5	1196	0.77	0.79	71	empty

Interfaces

14 interfaces between chains.

C–D · 718 Å² buried · 6 hydrogen bonds · protein-protein
A–B · 671 Å² buried · 7 hydrogen bonds · protein-protein
E–F · 665 Å² buried · 5 hydrogen bonds · protein-protein
G–H · 634 Å² buried · 7 hydrogen bonds · protein-protein
A–G · 308 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

4V0M · Crystal structure of BBS1N in complex with ARL6DN · the same entry in another collection · chain A against A, 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 A8JF99
Every structure of UniProt A8JEA1
Elsewhere: RCSB PDB 4V0M · PDBe 4V0M · UniProt A8JF99 · UniProt A8JEA1

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