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AP-1, Arf1, Nef lattice on MHC-I lipopeptide incorporated narrow membrane tubes, centered on gamma-Arf1

Analyse AP-1, Arf1, Nef lattice on MHC-I lipopeptide incorporated narrow membrane… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 8D9T
Type: protein
Length: 13,422 residues
Chains: 54
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 20.0
Source: Homo sapiens; Human immunodeficiency virus 1; Mus musculus
Molecule: ADP ribosylation factor 1; Protein Nef; HLA class I histocompatibility antigen, A alpha…
UniProt: A0A8C2UGL4, Q90VU7, P04439, Q10567, P22892, P35585, Q96PC3
Ligands: GTP, MG
Pockets: 20 · best druggability 0.72

Structure

electron microscopy · resolution 20.0 · 8 distinct chains · 51% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C, H, J, X, K, Z, O, a, P, b, Q, c	ADP ribosylation factor 1	protein	180	32% helix, 17% strand	A0A8C2UGL4
N, n, o, p, q, r	Protein Nef	protein	137	42% helix, 12% strand	Q90VU7
Y, x, y, z, 0, 1	HLA class I histocompatibility antigen, A alpha chain	protein	18	17% helix, 11% strand	P04439
B, A, D, E, F, I	AP-1 complex subunit beta-1	protein	570	68% helix, 0% strand	Q10567
G, R, T, U, V, W	AP-1 complex subunit gamma-1	protein	585	70% helix, 1% strand	P22892
L, d, e, f, g, h	Protein Nef	protein	10	0% helix, 0% strand	Q90VU7
M, i, j, k, l, m	AP-1 complex subunit mu-1	protein	415	17% helix, 38% strand	P35585
S, s, t, u, v, w	AP-1 complex subunit sigma-3	protein	142	45% helix, 22% strand	Q96PC3

Ligands and binding sites

GTP · Guanosine-5'-triphosphate · ligand · 12 copies · chains C, H, J, X, K, Z, O, a, P, b, Q, c
MG · Magnesium ion · metal · 12 copies · chains C, H, J, X, K, Z, O, a, P, b, Q, c

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	1075	0.72	0.76	166	empty
2	1190	0.71	0.76	160	empty
3	940	0.71	0.76	146	empty
4	913	0.71	0.77	143	empty
5	408	0.69	0.82	80	empty

Interfaces

66 interfaces between chains.

I–m · 469 Å² buried · 6 hydrogen bonds · protein-protein
E–k · 467 Å² buried · 6 hydrogen bonds · protein-protein
A–i · 467 Å² buried · 6 hydrogen bonds · protein-protein
B–M · 466 Å² buried · 6 hydrogen bonds · protein-protein
D–j · 462 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

Q96PC3 · AlphaFold monomer V2.0 prediction for ap-1 complex subunit sigma-3 (Q96PC3) · a predicted model of the same protein · chain u against A, TM-score 0.98
Q10567 · AlphaFold monomer V2.0 prediction for ap-1 complex subunit beta-1 (Q10567) · a predicted model of the same protein · chain D against A, TM-score 0.95

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 A0A8C2UGL4
Every structure of UniProt Q90VU7
Every structure of UniProt P04439
Every structure of UniProt Q10567
Every structure of UniProt P22892
Every structure of UniProt P35585
Every structure of UniProt Q96PC3
Elsewhere: RCSB PDB 8D9T · PDBe 8D9T · UniProt A0A8C2UGL4 · UniProt Q90VU7 · UniProt P04439 · UniProt Q10567 · UniProt P22892 · UniProt P35585 · UniProt Q96PC3

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