MolNFT v1 · #94115 · protein
Structural basis for recruitment and activation of the ap-1 clathrin adaptor complex by ARF1
4HMY · Ap-1 complex subunit gamma-1: “Structural basis for recruitment and activation of the ap-1 clathrin adaptor complex by ARF1”. X-ray diffraction, 2 ligands (GTP, MG), 20 pockets (best druggability 0.86). MolNFT v1 #94115 on…
- PDB
- 4HMY
- Type
- protein
- Length
- 1,835 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ap-1 complex subunit gamma-1; Ap-1 complex subunit beta-1; Ap-1 complex subunit mu-1…
- UniProt
- P22892, Q10567, P35585, Q96PC3, P84077
- Ligands
- GTP, MG
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 5 distinct chains · 49% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ap-1 complex subunit gamma-1 | protein | 579 | 65% helix, 0% strand | P22892 |
| B | Ap-1 complex subunit beta-1 | protein | 563 | 63% helix, 0% strand | Q10567 |
| M | Ap-1 complex subunit mu-1 | protein | 383 | 16% helix, 32% strand | P35585 |
| S | Ap-1 complex subunit sigma-3 | protein | 145 | 39% helix, 26% strand | Q96PC3 |
| C | ADP-ribosylation factor 1 | protein | 165 | 33% helix, 22% strand | P84077 |
Ligands and binding sites
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 | 518 | 0.86 | 0.91 | 91 | empty |
| 2 | 1093 | 0.82 | 0.83 | 141 | empty |
| 3 | 119 | 0.81 | 0.99 | 22 | empty |
| 4 | 891 | 0.79 | 0.82 | 118 | empty |
| 5 | 120 | 0.79 | 0.96 | 32 | empty |
Interfaces
7 interfaces between chains.
- B–M · 3455 Ų buried · 29 hydrogen bonds · protein-protein
- A–S · 2894 Ų buried · 39 hydrogen bonds · protein-protein
- A–B · 1554 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 870 Ų buried · 5 hydrogen bonds · protein-protein
- M–S · 262 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4HMY · Structural basis for recruitment and activation of the AP-1 clathrin adaptor complex by… · the same entry in another collection · chain C against C, 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 0.96
- P84077 · AlphaFold monomer V2.0 prediction for ADP-ribosylation factor 1 (P84077) · a predicted model of the same protein · chain C against A, TM-score 0.95
- P35585 · AlphaFold monomer V2.0 prediction for ap-1 complex subunit mu-1 (P35585) · a predicted model of the same protein · chain M against A, TM-score 0.91
- 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 0.85
- P22892 · AlphaFold monomer V2.0 prediction for ap-1 complex subunit gamma-1 (P22892) · a predicted model of the same protein · chain A against A, TM-score 0.74
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 P22892
- Every structure of UniProt Q10567
- Every structure of UniProt P35585
- Every structure of UniProt Q96PC3
- Every structure of UniProt P84077
- Elsewhere: RCSB PDB 4HMY · PDBe 4HMY · UniProt P22892 · UniProt Q10567 · UniProt P35585 · UniProt Q96PC3 · UniProt P84077
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