MolNFT v1 · #146118 · protein
Structure of the cargo bound ap-1:ARF1:TETHERIN-nef (L164A, L165A) dileucine mutant dimer
6D84 · Bone marrow stromal antigen 2,PROTEIN nef: “Structure of the cargo bound ap-1:ARF1:TETHERIN-nef (L164A, L165A) dileucine mutant dimer”. Electron microscopy, 2 ligands (GTP, MG), 20 pockets (best druggability 0.75). MolNFT v1 #146118…
- PDB
- 6D84
- Type
- protein
- Length
- 4,126 residues
- Chains
- 16
- 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 0.75
Structure
electron microscopy · 8 distinct chains · 49% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| T, R | Bone marrow stromal antigen 2,PROTEIN nef | protein | 13 | 0% helix, 15% strand | Q10589, Q90VU7 |
| L, O | Bone marrow stromal antigen 2,PROTEIN nef | protein | 10 | 0% helix, 0% strand | Q10589, Q90VU7 |
| B, F | Ap-1 complex subunit beta-1 | protein | 570 | 67% helix, 0% strand | Q10567 |
| C, I | ADP-ribosylation factor 1 | protein | 165 | 30% helix, 21% strand | P84077 |
| G, K | Ap-1 complex subunit gamma-1 | protein | 585 | 67% helix, 1% strand | P22892 |
| H, N | ADP-ribosylation factor 1 | protein | 163 | 33% helix, 27% strand | P84077 |
| M, P | Ap-1 complex subunit mu-1 | protein | 415 | 17% helix, 40% strand | P35585 |
| S, Q | Ap-1 complex subunit sigma-3 | protein | 142 | 45% helix, 23% strand | Q96PC3 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 4 copies · chains C, H, I, N
- MG · Magnesium ion · metal · 4 copies · chains C, H, I, N
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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 715 | 0.75 | 0.80 | 69 | empty |
| 2 | 713 | 0.75 | 0.80 | 65 | empty |
| 3 | 318 | 0.73 | 0.86 | 40 | empty |
| 4 | 1195 | 0.73 | 0.76 | 115 | empty |
| 5 | 57 | 0.71 | 0.98 | 19 | empty |
Interfaces
30 interfaces between chains.
- B–M · 4149 Ų buried · 44 hydrogen bonds · protein-protein
- F–P · 4142 Ų buried · 44 hydrogen bonds · protein-protein
- K–Q · 3199 Ų buried · 37 hydrogen bonds · protein-protein
- G–S · 3186 Ų buried · 37 hydrogen bonds · protein-protein
- F–K · 1671 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 6D84 · Structure of the cargo bound AP-1:Arf1:tetherin-Nef (L164A, L165A) dileucine mutant dimer · the same entry in another collection · chain F against F, 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 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 6D84 · PDBe 6D84 · UniProt Q10589 · UniProt Q90VU7 · UniProt Q10567 · UniProt P84077 · UniProt P22892 · UniProt P35585 · UniProt Q96PC3
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