MolNFT v1 · #182553 · protein
ERAP1 binds peptide C-terminus of a spf sequence (fkarkf)
7MWB · Endoplasmic reticulum aminopeptidase 1,SPF sequence: “ERAP1 binds peptide C-terminus of a spf sequence (fkarkf)”. X-ray diffraction, 18 pockets (best druggability 0.81). MolNFT v1 #182553 on GenesisL1: 3D structure, binding sites…
- PDB
- 7MWB
- Type
- protein
- Length
- 1,628 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endoplasmic reticulum aminopeptidase 1,SPF sequence
- EC
- 3.4.11.-, 3.4.1.1
- UniProt
- Q9NZ08
- Pockets
- 18 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 59% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endoplasmic reticulum aminopeptidase 1,SPF sequence (EC 3.4.11.-, 3.4.1.1) | protein | 407 | 59% helix, 11% strand | Q9NZ08 |
| B | Endoplasmic reticulum aminopeptidase 1,SPF sequence (EC 3.4.11.-, 3.4.1.1) | protein | 408 | 60% helix, 10% strand | Q9NZ08 |
| C | Endoplasmic reticulum aminopeptidase 1,SPF sequence (EC 3.4.11.-, 3.4.1.1) | protein | 407 | 59% helix, 10% strand | Q9NZ08 |
| D | Endoplasmic reticulum aminopeptidase 1,SPF sequence (EC 3.4.11.-, 3.4.1.1) | protein | 406 | 60% helix, 10% strand | Q9NZ08 |
Pockets
18 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1030 | 0.81 | 0.82 | 88 | empty |
| 2 | 901 | 0.79 | 0.82 | 85 | empty |
| 3 | 859 | 0.69 | 0.75 | 64 | empty |
| 4 | 547 | 0.66 | 0.77 | 49 | empty |
| 5 | 510 | 0.63 | 0.76 | 55 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1371 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 1285 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 54 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7MWB · ERAP1 binds peptide C-terminus of a SPF sequence (FKARKF) · the same entry in another collection · chain B against B, TM-score 1.00
- Q9NZ08 · AlphaFold monomer V2.0 prediction for endoplasmic reticulum aminopeptidase 1 (Q9NZ08) · a predicted model of the same protein · chain C against A, TM-score 0.95
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 Q9NZ08
- Elsewhere: RCSB PDB 7MWB · PDBe 7MWB · UniProt Q9NZ08
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