MolNFT v1 · #137090 · protein
Crystal structure of CU(I)-loaded yeast ATX1: crystal form II
5VDF · Metal homeostasis factor ATX1: “Crystal structure of CU(I)-loaded yeast ATX1: crystal form II”. X-ray diffraction, 1 ligand (CU1), 5 pockets (best druggability 0.69). MolNFT v1 #137090 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5VDF
- Type
- protein
- Length
- 565 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Metal homeostasis factor ATX1
- UniProt
- P38636
- Ligands
- CU1
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E, H | Metal homeostasis factor ATX1 | protein | 72 | 29% helix, 35% strand | P38636 |
| C | Metal homeostasis factor ATX1 | protein | 68 | 31% helix, 37% strand | P38636 |
| F | Metal homeostasis factor ATX1 | protein | 70 | 30% helix, 36% strand | P38636 |
| G | Metal homeostasis factor ATX1 | protein | 67 | 30% helix, 37% strand | P38636 |
Ligands and binding sites
- CU1 · Copper (I) ion · metal · 4 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 585 | 0.69 | 0.78 | 64 | empty |
| 2 | 321 | 0.58 | 0.76 | 36 | empty |
| 3 | 215 | 0.53 | 0.77 | 26 | empty |
| 4 | 197 | 0.50 | 0.76 | 23 | empty |
| 5 | 199 | 0.48 | 0.75 | 19 | empty |
Interfaces
12 interfaces between chains.
- E–F · 486 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 478 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 466 Ų buried · 4 hydrogen bonds · protein-protein
- G–H · 430 Ų buried · 2 hydrogen bonds · protein-protein
- A–F · 345 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5VDF · Crystal Structure of Cu(I)-loaded yeast Atx1: Crystal Form II · the same entry in another collection · chain H against H, TM-score 1.00
- P38636 · AlphaFold monomer V2.0 prediction for metal homeostasis factor ATX1 (P38636) · a predicted model of the same protein · chain H against A, TM-score 0.98
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 P38636
- Elsewhere: RCSB PDB 5VDF · PDBe 5VDF · UniProt P38636
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