MolNFT v1 · #172776 · protein
Crystal structure of human complement C5 in complex with the K8 bovine knob domain peptide.
7AD7: “Crystal structure of human complement C5 in complex with the K8 bovine knob domain peptide.”. X-ray diffraction, 4 ligands (MHA, CYS, TAM), 20 pockets (best druggability 0.78). MolNFT v1 #172776 on GenesisL1: 3D structure, binding…
- PDB
- 7AD7
- Type
- protein
- Length
- 1,469 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Complement C5; K8 peptide
- UniProt
- P01031
- Ligands
- MHA, CYS, TAM, NAG
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Complement C5 | protein | 635 | 5% helix, 50% strand | P01031 |
| A | Complement C5 | protein | 782 | 30% helix, 30% strand | P01031 |
| C | K8 peptide | protein | 52 | 0% helix, 48% strand | — |
Ligands and binding sites
- MHA · (carbamoylmethyl-carboxymethyl-amino)-acetic acid · ligand · chains B
- CYS · Cysteine · ligand · chains A
- TAM · Tris(hydroxyethyl)aminomethane · ligand · chains C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- EOH · Ethanol · additive · 4 copies · chains B, A, C
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1039 | 0.78 | 0.80 | 90 | MPD |
| 2 | 926 | 0.70 | 0.75 | 74 | empty |
| 3 | 497 | 0.70 | 0.80 | 69 | empty |
| 4 | 592 | 0.67 | 0.76 | 63 | empty |
| 5 | 90 | 0.64 | 0.90 | 17 | empty |
Interfaces
2 interfaces between chains.
- B–A · 3993 Ų buried · 62 hydrogen bonds · protein-protein
- A–C · 851 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 1 covalent, 1 glycan (disulfide, covalent ligand, N-glycosylation).
Compared structures
- 7AD7 · Crystal structure of human complement C5 in complex with the K8 bovine knob domain… · the same entry in another collection · chain B against B, TM-score 1.00
- P01031 · AlphaFold monomer V2.0 prediction for complement C5 (P01031) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P01031
- Elsewhere: RCSB PDB 7AD7 · PDBe 7AD7 · UniProt P01031
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