Research workbench
Cryo-EM structure of trimeric human STEAP1 bound to three FAB120.545 fragments
Analyse Cryo-EM structure of trimeric human STEAP1 bound to three FAB120.545 fragments in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Y9B
- Type
- protein
- Length
- 1,434 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Metalloreductase STEAP1; FAB120.545 light chain; FAB120.545 heavy chain
- EC
- 1.16.1.-
- UniProt
- Q9UHE8
- Ligands
- HEM, XP4
- Pockets
- 17 · best druggability 0.86
Structure
electron microscopy · 3 distinct chains · 41% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, A, B | Metalloreductase STEAP1 (EC 1.16.1.-) | protein | 244 | 77% helix, 0% strand | Q9UHE8 |
| L, M, N | FAB120.545 light chain | protein | 113 | 3% helix, 48% strand | — |
| H, I, J | FAB120.545 heavy chain | protein | 121 | 5% helix, 45% strand | — |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 3 copies · chains C, B, A
- XP4 · 1,2-dimyristoyl-sn-glycero-3-phosphate · ligand · 3 copies · chains C, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 672 | 0.86 | 0.90 | 84 | HEM |
| 2 | 680 | 0.85 | 0.89 | 67 | HEM |
| 3 | 1158 | 0.84 | 0.85 | 86 | HEM |
| 4 | 1147 | 0.79 | 0.80 | 92 | empty |
| 5 | 89 | 0.58 | 0.86 | 13 | empty |
Interfaces
21 interfaces between chains.
- C–A · 1803 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1793 Ų buried · 15 hydrogen bonds · protein-protein
- C–B · 1775 Ų buried · 15 hydrogen bonds · protein-protein
- L–H · 1056 Ų buried · 10 hydrogen bonds · protein-protein
- J–N · 1050 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 6Y9B · Cryo-EM structure of trimeric human STEAP1 bound to three Fab120.545 fragments · the same entry in another collection · chain B against B, TM-score 1.00
- Q9UHE8 · AlphaFold monomer V2.0 prediction for metalloreductase STEAP1 (Q9UHE8) · a predicted model of the same protein · chain C 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 Q9UHE8
- Elsewhere: RCSB PDB 6Y9B · PDBe 6Y9B · UniProt Q9UHE8
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