Research workbench
Cryoem structure of 3C9-smac
Analyse Cryoem structure of 3C9-smac in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NYC
- Type
- protein
- Length
- 5,312 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Complement component C7; Complement component C8 beta chain; Complement component C8…
- UniProt
- P10643, P07358, P07357, P02748, P13671, P01031, P07360
- Ligands
- NAG, BMA, FUC, CA
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 9 distinct chains · 17% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Complement component C7 | protein | 809 | 14% helix, 36% strand | P10643 |
| D | Complement component C8 beta chain | protein | 487 | 16% helix, 39% strand | P07358 |
| E | Complement component C8 alpha chain | protein | 482 | 16% helix, 36% strand | P07357 |
| G | Complement component C9 | protein | 393 | 20% helix, 32% strand | P02748 |
| B | Complement component C6 | protein | 718 | 13% helix, 36% strand | P13671 |
| H | Complement component C9 | protein | 404 | 19% helix, 34% strand | P02748 |
| A | Complement C5 | protein | 1542 | 17% helix, 36% strand | P01031 |
| F | Complement component C8 gamma chain | protein | 168 | 16% helix, 39% strand | P07360 |
| I | Complement component C9 | protein | 309 | 25% helix, 26% strand | P02748 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains C, D, A, E, G, H, B
- BMA · beta-D-mannopyranose · sugar · 8 copies · chains C, D, E, G, H
- FUC · alpha-L-fucopyranose · sugar · chains C, B
- CA · Calcium ion · metal · 3 copies · chains D, E, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1161 | 0.88 | 0.90 | 136 | empty |
| 2 | 841 | 0.87 | 0.89 | 110 | empty |
| 3 | 1100 | 0.85 | 0.86 | 125 | empty |
| 4 | 1000 | 0.84 | 0.85 | 135 | empty |
| 5 | 910 | 0.83 | 0.85 | 97 | BMA |
Interfaces
14 interfaces between chains.
- C–B · 4839 Ų buried · 100 hydrogen bonds · protein-protein
- C–D · 3969 Ų buried · 95 hydrogen bonds · protein-protein
- D–E · 3893 Ų buried · 95 hydrogen bonds · protein-protein
- B–A · 3666 Ų buried · 45 hydrogen bonds · protein-protein
- E–G · 3424 Ų buried · 61 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 103 disulfide, 13 glycan (disulfide, C-mannosylation, N-glycosylation).
Compared structures
- P07360 · AlphaFold monomer V2.0 prediction for complement component C8 gamma chain (P07360) · a predicted model of the same protein · chain F against A, TM-score 0.95
- P02748 · AlphaFold monomer V2.0 prediction for complement component C9 (P02748) · a predicted model of the same protein · chain I against A, TM-score 0.86
- P07358 · AlphaFold monomer V2.0 prediction for complement component C8 beta chain (P07358) · a predicted model of the same protein · chain D against A, TM-score 0.81
- P07357 · AlphaFold monomer V2.0 prediction for complement component C8 alpha chain (P07357) · a predicted model of the same protein · chain E against A, TM-score 0.76
- P13671 · AlphaFold monomer V2.0 prediction for complement component C6 (P13671) · a predicted model of the same protein · chain B against A, TM-score 0.57
- P01031 · AlphaFold monomer V2.0 prediction for complement C5 (P01031) · a predicted model of the same protein · chain A against A, TM-score 0.56
- P10643 · AlphaFold monomer V2.0 prediction for complement component C7 (P10643) · a predicted model of the same protein · chain C against A, TM-score 0.48
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 P10643
- Every structure of UniProt P07358
- Every structure of UniProt P07357
- Every structure of UniProt P02748
- Every structure of UniProt P13671
- Every structure of UniProt P01031
- Every structure of UniProt P07360
- Elsewhere: RCSB PDB 7NYC · PDBe 7NYC · UniProt P10643 · UniProt P07358 · UniProt P07357 · UniProt P02748 · UniProt P13671 · UniProt P01031 · UniProt P07360
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