MolNFT v1 · #121580 · protein
Structure of human C4B-binding protein alpha chain ccp domains 1 and 2 in complex with the hypervariable region of group a streptococcus M49 protein.
5HZP · M protein, serotype 49: “Structure of human C4B-binding protein alpha chain ccp domains 1 and 2 in complex with the hypervariable…”. X-ray diffraction, 1 ligand (PO4), 3 pockets (best druggability 0.52). MolNFT v1 #121580 on…
- PDB
- 5HZP
- Type
- protein
- Length
- 392 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- M protein, serotype 49; C4B-binding protein alpha chain
- UniProt
- P16947, P04003
- Ligands
- PO4
- Pockets
- 3 · best druggability 0.52
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, A | M protein, serotype 49 | protein | 71 | 89% helix, 0% strand | P16947 |
| B, D | C4B-binding protein alpha chain | protein | 125 | 0% helix, 41% strand | P04003 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 5 copies · chains C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 258 | 0.52 | 0.75 | 35 | empty |
| 2 | 113 | 0.39 | 0.75 | 15 | empty |
| 3 | 65 | 0.29 | 0.74 | 16 | empty |
Interfaces
5 interfaces between chains.
- C–A · 1083 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 830 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 806 Ų buried · 8 hydrogen bonds · protein-protein
- C–B · 133 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 131 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 6 modified (disulfide, engineered).
Compared structures
- 5HZP · Structure of human C4b-binding protein alpha chain CCP domains 1 and 2 in complex with… · the same entry in another collection · chain B against B, TM-score 1.00
- P04003 · AlphaFold monomer V2.0 prediction for C4B-binding protein alpha chain (P04003) · a predicted model of the same protein · chain D against A, TM-score 0.95
- P16947 · AlphaFold monomer V2.0 prediction for M protein, serotype 49 (P16947) · a predicted model of the same protein · chain C against A, TM-score 0.93
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 P16947
- Every structure of UniProt P04003
- Elsewhere: RCSB PDB 5HZP · PDBe 5HZP · UniProt P16947 · UniProt P04003
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