Research workbench

Structure of the cargo bound ap-1:ARF1:TETHERIN-nef monomer

Analyse Structure of the cargo bound ap-1:ARF1:TETHERIN-nef monomer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6DFF
Type: protein
Length: 2,063 residues
Chains: 8
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Bone marrow stromal antigen 2, nef protein chimera; Ap-1 complex subunit beta-1…
UniProt: Q10589, Q90VU7, Q10567, P84077, P22892, P35585, Q96PC3
Ligands: GTP, MG
Pockets: 20 · best druggability 0.73

Structure

electron microscopy · 8 distinct chains · 47% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	Bone marrow stromal antigen 2, nef protein chimera	protein	10	0% helix, 0% strand	Q10589, Q90VU7
T	Bone marrow stromal antigen 2, nef protein chimera	protein	13	0% helix, 15% strand	Q10589, Q90VU7
B	Ap-1 complex subunit beta-1	protein	570	63% helix, 0% strand	Q10567
C	ADP-ribosylation factor 1	protein	165	27% helix, 20% strand	P84077
G	Ap-1 complex subunit gamma-1	protein	585	66% helix, 0% strand	P22892
H	ADP-ribosylation factor 1	protein	163	29% helix, 25% strand	P84077
M	Ap-1 complex subunit mu-1	protein	415	16% helix, 38% strand	P35585
S	Ap-1 complex subunit sigma-3	protein	142	42% helix, 17% strand	Q96PC3

Ligands and binding sites

GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains C, H
MG · Magnesium ion · metal · 2 copies · chains C, H

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	63	0.73	0.98	17	empty
2	67	0.72	0.97	17	empty
3	639	0.71	0.79	65	empty
4	747	0.71	0.77	92	empty
5	229	0.71	0.87	26	empty

Interfaces

11 interfaces between chains.

B–M · 4252 Å² buried · 46 hydrogen bonds · protein-protein
G–S · 3123 Å² buried · 22 hydrogen bonds · protein-protein
B–G · 1641 Å² buried · 23 hydrogen bonds · protein-protein
B–C · 1036 Å² buried · 4 hydrogen bonds · protein-protein
G–H · 849 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

6DFF · Structure of the cargo bound AP-1:Arf1:tetherin-Nef monomer · the same entry in another collection · chain S against S, TM-score 1.00
Q96PC3 · AlphaFold monomer V2.0 prediction for ap-1 complex subunit sigma-3 (Q96PC3) · a predicted model of the same protein · chain S against A, TM-score 0.98
P84077 · AlphaFold monomer V2.0 prediction for ADP-ribosylation factor 1 (P84077) · a predicted model of the same protein · chain H against A, TM-score 0.96
Q10567 · AlphaFold monomer V2.0 prediction for ap-1 complex subunit beta-1 (Q10567) · a predicted model of the same protein · chain B against A, TM-score 0.95
P22892 · AlphaFold monomer V2.0 prediction for ap-1 complex subunit gamma-1 (P22892) · a predicted model of the same protein · chain G against A, TM-score 0.94

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 Q10589
Every structure of UniProt Q90VU7
Every structure of UniProt Q10567
Every structure of UniProt P84077
Every structure of UniProt P22892
Every structure of UniProt P35585
Every structure of UniProt Q96PC3
Elsewhere: RCSB PDB 6DFF · PDBe 6DFF · UniProt Q10589 · UniProt Q90VU7 · UniProt Q10567 · UniProt P84077 · UniProt P22892 · UniProt P35585 · UniProt Q96PC3

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