Research workbench
Structure of the cargo bound ap-1:ARF1:TETHERIN-nef stable closed trimer
Analyse Structure of the cargo bound ap-1:ARF1:TETHERIN-nef stable closed trimer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CRI
- Type
- protein
- Length
- 6,582 residues
- Chains
- 24
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bone marrow stromal antigen 2, protein nef chimera; Ap-1 complex subunit beta-1…
- UniProt
- Q10589, Q90VU7, Q10567, P84077, P22892, P35585, Q96PC3
- Ligands
- GTP, MG
- Pockets
- 20 · best druggability 0.76
Structure
electron microscopy · 8 distinct chains · 48% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| T, c, d | Bone marrow stromal antigen 2, protein nef chimera | protein | 13 | 0% helix, 8% strand | Q10589, Q90VU7 |
| B, I, J | Ap-1 complex subunit beta-1 | protein | 570 | 66% helix, 0% strand | Q10567 |
| C, K, L | ADP-ribosylation factor 1 | protein | 165 | 28% helix, 19% strand | P84077 |
| G, Q, R | Ap-1 complex subunit gamma-1 | protein | 585 | 68% helix, 1% strand | P22892 |
| H, U, V | ADP-ribosylation factor 1 | protein | 163 | 31% helix, 26% strand | P84077 |
| M, W, X | Ap-1 complex subunit mu-1 | protein | 415 | 17% helix, 40% strand | P35585 |
| S, a, b | Ap-1 complex subunit sigma-3 | protein | 142 | 44% helix, 21% strand | Q96PC3 |
| N, Y, Z | Bone marrow stromal antigen 2, protein nef chimera | protein | 141 | 31% helix, 12% strand | Q10589, Q90VU7 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 6 copies · chains C, H, K, U, L, V
- MG · Magnesium ion · metal · 6 copies · chains C, H, K, U, L, V
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 | 356 | 0.76 | 0.86 | 47 | empty |
| 2 | 362 | 0.76 | 0.86 | 43 | empty |
| 3 | 345 | 0.76 | 0.87 | 39 | empty |
| 4 | 70 | 0.75 | 0.98 | 21 | empty |
| 5 | 77 | 0.74 | 0.98 | 19 | empty |
Interfaces
40 interfaces between chains.
- J–X · 4091 Ų buried · 45 hydrogen bonds · protein-protein
- I–W · 4091 Ų buried · 44 hydrogen bonds · protein-protein
- B–M · 4089 Ų buried · 44 hydrogen bonds · protein-protein
- R–b · 2973 Ų buried · 29 hydrogen bonds · protein-protein
- Q–a · 2971 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 6CRI · Structure of the cargo bound AP-1:Arf1:tetherin-Nef stable closed trimer · the same entry in another collection · chain G against G, 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 6CRI · PDBe 6CRI · UniProt Q10589 · UniProt Q90VU7 · UniProt Q10567 · UniProt P84077 · UniProt P22892 · UniProt P35585 · UniProt Q96PC3
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