MolNFT v1 · #184790 · protein
Human signal peptidase complex paralog a (spc-a)
7P2P · Signal peptidase complex catalytic subunit SEC11A: “Human signal peptidase complex paralog a (spc-a)”. Electron microscopy, 3 ligands (NAG, MAN, BMA), 13 pockets (best druggability 0.79). MolNFT v1 #184790 on GenesisL1: 3D…
- PDB
- 7P2P
- Type
- protein
- Length
- 587 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Signal peptidase complex catalytic subunit SEC11A; Signal peptidase complex subunit 3…
- EC
- 3.4.21.89, 3.4.-.-
- UniProt
- P67812, P61009, Q15005, Q9Y6A9
- Ligands
- NAG, MAN, BMA
- Pockets
- 13 · best druggability 0.79
Structure
electron microscopy · 4 distinct chains · 34% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Signal peptidase complex catalytic subunit SEC11A (EC 3.4.21.89) | protein | 148 | 24% helix, 23% strand | P67812 |
| B | Signal peptidase complex subunit 3 (EC 3.4.-.-) | protein | 179 | 14% helix, 33% strand | P61009 |
| C | Signal peptidase complex subunit 2 (EC 3.4.-.-) | protein | 174 | 49% helix, 20% strand | Q15005 |
| D | Signal peptidase complex subunit 1 (EC 3.4.-.-) | protein | 86 | 64% helix, 0% strand | Q9Y6A9 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains B
- MAN · alpha-D-mannopyranose · sugar · 2 copies
- BMA · beta-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 859 | 0.79 | 0.81 | 87 | empty |
| 2 | 297 | 0.78 | 0.90 | 55 | empty |
| 3 | 128 | 0.78 | 0.96 | 25 | empty |
| 4 | 556 | 0.77 | 0.83 | 60 | empty |
| 5 | 136 | 0.71 | 0.90 | 24 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1177 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 884 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 673 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 563 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 105 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 glycan (N-glycosylation).
Compared structures
- 7P2P · Human Signal Peptidase Complex Paralog A (SPC-A) · the same entry in another collection · chain D against D, TM-score 1.00
- P67812 · AlphaFold monomer V2.0 prediction for signal peptidase complex catalytic subunit SEC11A… · a predicted model of the same protein · chain A against A, TM-score 0.85
- P61009 · AlphaFold monomer V2.0 prediction for signal peptidase complex subunit 3 (P61009) · a predicted model of the same protein · chain B against A, TM-score 0.85
- Q15005 · AlphaFold monomer V2.0 prediction for signal peptidase complex subunit 2 (Q15005) · a predicted model of the same protein · chain C against A, TM-score 0.77
- Q9Y6A9 · AlphaFold monomer V2.0 prediction for signal peptidase complex subunit 1 (Q9Y6A9) · a predicted model of the same protein · chain D against A, TM-score 0.62
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 P67812
- Every structure of UniProt P61009
- Every structure of UniProt Q15005
- Every structure of UniProt Q9Y6A9
- Elsewhere: RCSB PDB 7P2P · PDBe 7P2P · UniProt P67812 · UniProt P61009 · UniProt Q15005 · UniProt Q9Y6A9
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