MolNFT v1 · #137089 · protein
Crystal structure of CU(I)-loaded yeast ATX1: crystal form I
5VDE · Metal homeostasis factor ATX1: “Crystal structure of CU(I)-loaded yeast ATX1: crystal form I”. X-ray diffraction, 1 ligand (CU1), 2 pockets (best druggability 0.63). MolNFT v1 #137089 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5VDE
- Type
- protein
- Length
- 284 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Metal homeostasis factor ATX1
- UniProt
- P38636
- Ligands
- CU1
- Pockets
- 2 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Metal homeostasis factor ATX1 | protein | 71 | 30% helix, 37% strand | P38636 |
| B | Metal homeostasis factor ATX1 | protein | 72 | 29% helix, 36% strand | P38636 |
| D | Metal homeostasis factor ATX1 | protein | 70 | 30% helix, 37% strand | P38636 |
Ligands and binding sites
- CU1 · Copper (I) ion · metal · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 549 | 0.63 | 0.75 | 54 | empty |
| 2 | 50 | 0.32 | 0.77 | 8 | empty |
Interfaces
4 interfaces between chains.
- C–D · 488 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 478 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 306 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 297 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5VDE · Crystal Structure of Cu(I)-loaded yeast Atx1: Crystal Form I · the same entry in another collection · chain D against D, TM-score 1.00
- P38636 · AlphaFold monomer V2.0 prediction for metal homeostasis factor ATX1 (P38636) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 5VDE · PDBe 5VDE · UniProt P38636
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