Research workbench
Human signal peptidase complex paralog C (spc-C)
Analyse Human signal peptidase complex paralog C (spc-C) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7P2Q
- Type
- protein
- Length
- 587 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Signal peptidase complex catalytic subunit SEC11C; Signal peptidase complex subunit 3…
- EC
- 3.4.21.89, 3.4.-.-
- UniProt
- Q9BY50, P61009, Q15005, Q9Y6A9
- Ligands
- NAG, MAN, BMA
- Pockets
- 13 · best druggability 0.80
Structure
electron microscopy · 4 distinct chains · 37% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Signal peptidase complex catalytic subunit SEC11C (EC 3.4.21.89) | protein | 148 | 26% helix, 27% strand | Q9BY50 |
| B | Signal peptidase complex subunit 3 (EC 3.4.-.-) | protein | 179 | 16% helix, 28% strand | P61009 |
| C | Signal peptidase complex subunit 2 (EC 3.4.-.-) | protein | 174 | 52% helix, 20% strand | Q15005 |
| D | Signal peptidase complex subunit 1 (EC 3.4.-.-) | protein | 86 | 69% 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 · chains B
- BMA · beta-D-mannopyranose · sugar · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 671 | 0.80 | 0.84 | 77 | empty |
| 2 | 707 | 0.74 | 0.79 | 76 | empty |
| 3 | 93 | 0.72 | 0.94 | 21 | empty |
| 4 | 152 | 0.66 | 0.86 | 29 | empty |
| 5 | 64 | 0.64 | 0.92 | 17 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1479 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 919 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 683 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 677 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 32 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 glycan (N-glycosylation).
Compared structures
- 7P2Q · Human Signal Peptidase Complex Paralog C (SPC-C) · the same entry in another collection · chain D against D, TM-score 1.00
- Q9BY50 · AlphaFold monomer V2.0 prediction for signal peptidase complex catalytic subunit SEC11C… · a predicted model of the same protein · chain A against A, TM-score 0.84
- 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 0.83
- 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 0.79
- 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 Q9BY50
- Every structure of UniProt P61009
- Every structure of UniProt Q15005
- Every structure of UniProt Q9Y6A9
- Elsewhere: RCSB PDB 7P2Q · PDBe 7P2Q · UniProt Q9BY50 · UniProt P61009 · UniProt Q15005 · UniProt Q9Y6A9
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