Research workbench
Molecular basis for complement recognition and inhibition determined by crystallographic studies of the staphylococcal complement inhibitor (scin) bound to C3C and C3B
Analyse Molecular basis for complement recognition and inhibition determined by… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OHX
- Type
- protein
- Length
- 2,406 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Complement C3; Staphylococcal complement inhibitor
- UniProt
- P01024, Q931M7
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 5 distinct chains · 12% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Complement C3 | protein | 641 | 6% helix, 50% strand | P01024 |
| B, E | Complement C3 | protein | 184 | 2% helix, 53% strand | P01024 |
| C | Complement C3 | protein | 293 | 13% helix, 32% strand | P01024 |
| M, P | Staphylococcal complement inhibitor | protein | 84 | 81% helix, 0% strand | Q931M7 |
| F | Complement C3 | protein | 295 | 10% helix, 32% strand | P01024 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, D
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 | 1198 | 0.80 | 0.82 | 90 | empty |
| 2 | 102 | 0.74 | 0.96 | 26 | empty |
| 3 | 559 | 0.73 | 0.81 | 72 | empty |
| 4 | 793 | 0.73 | 0.78 | 72 | empty |
| 5 | 635 | 0.72 | 0.79 | 47 | empty |
Interfaces
18 interfaces between chains.
- A–B · 3562 Ų buried · 54 hydrogen bonds · protein-protein
- E–D · 3559 Ų buried · 55 hydrogen bonds · protein-protein
- A–D · 1379 Ų buried · 5 hydrogen bonds · protein-protein
- E–F · 1203 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 1179 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide (disulfide).
Compared structures
- 3OHX · Molecular Basis for Complement Recognition and Inhibition Determined by Crystallographic… · the same entry in another collection · chain D against D, TM-score 1.00
- P01024 · AlphaFold monomer V2.0 prediction for complement C3 (P01024) · a predicted model of the same protein · chain D against A, TM-score 0.98
- Q931M7 · AlphaFold monomer V2.0 prediction for staphylococcal complement inhibitor (Q931M7) · a predicted model of the same protein · chain M against A, TM-score 0.97
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 P01024
- Every structure of UniProt Q931M7
- Elsewhere: RCSB PDB 3OHX · PDBe 3OHX · UniProt P01024 · UniProt Q931M7
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