MolNFT v1 · #146117 · protein
Structure of the cargo bound ap-1:ARF1:TETHERIN-nef (L164A, L165A) dileucine mutant dimer monomeric subunit
6D83 · Bone marrow stromal antigen 2,PROTEIN nef: “Structure of the cargo bound ap-1:ARF1:TETHERIN-nef (L164A, L165A) dileucine mutant dimer monomeric subunit”. Electron microscopy, 2 ligands (GTP, MG), 20 pockets (best druggability 0.76).…
- PDB
- 6D83
- 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,PROTEIN nef; Ap-1 complex subunit beta-1; ADP-ribosylation…
- UniProt
- Q10589, Q90VU7, Q10567, P84077, P22892, P35585, Q96PC3
- Ligands
- GTP, MG
- Pockets
- 20 · best druggability 0.76
Structure
electron microscopy · 8 distinct chains · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| T | Bone marrow stromal antigen 2,PROTEIN nef | protein | 13 | 0% helix, 15% strand | Q10589, Q90VU7 |
| L | Bone marrow stromal antigen 2,PROTEIN nef | protein | 10 | 0% helix, 0% strand | Q10589, Q90VU7 |
| B | Ap-1 complex subunit beta-1 | protein | 570 | 63% helix, 0% strand | Q10567 |
| C | ADP-ribosylation factor 1 | protein | 165 | 29% helix, 20% strand | P84077 |
| G | Ap-1 complex subunit gamma-1 | protein | 585 | 66% helix, 1% strand | P22892 |
| H | ADP-ribosylation factor 1 | protein | 163 | 33% helix, 23% strand | P84077 |
| M | Ap-1 complex subunit mu-1 | protein | 415 | 17% helix, 41% strand | P35585 |
| S | Ap-1 complex subunit sigma-3 | protein | 142 | 43% helix, 23% 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, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 699 | 0.76 | 0.81 | 66 | empty |
| 2 | 354 | 0.75 | 0.86 | 39 | empty |
| 3 | 737 | 0.71 | 0.77 | 87 | empty |
| 4 | 50 | 0.70 | 0.98 | 14 | empty |
| 5 | 60 | 0.69 | 0.96 | 17 | empty |
Interfaces
11 interfaces between chains.
- B–M · 4315 Ų buried · 47 hydrogen bonds · protein-protein
- G–S · 3227 Ų buried · 30 hydrogen bonds · protein-protein
- B–G · 1670 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 991 Ų buried · 8 hydrogen bonds · protein-protein
- T–M · 835 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6D83 · Structure of the cargo bound AP-1:Arf1:tetherin-Nef (L164A, L165A) dileucine mutant dimer… · 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 0.94
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 6D83 · PDBe 6D83 · UniProt Q10589 · UniProt Q90VU7 · UniProt Q10567 · UniProt P84077 · UniProt P22892 · UniProt P35585 · UniProt Q96PC3
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