MolNFT v1 · #100218 · protein
Crystal structure of pfba, a surface adhesin of streptococcus pneumoniae
4MR0 · Plasmin and fibronectin-binding protein a: “Crystal structure of pfba, a surface adhesin of streptococcus pneumoniae”. X-ray diffraction, 3 ligands (MN, CA, CL), 5 pockets (best druggability 0.76). MolNFT v1 #100218 on GenesisL1: 3D…
- PDB
- 4MR0
- Type
- protein
- Length
- 902 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Plasmin and fibronectin-binding protein a
- UniProt
- Q8CYC9
- Ligands
- MN, CA, CL
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Plasmin and fibronectin-binding protein a | protein | 456 | 6% helix, 45% strand | Q8CYC9 |
| B | Plasmin and fibronectin-binding protein a | protein | 446 | 5% helix, 44% strand | Q8CYC9 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 8 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- BME · Beta-mercaptoethanol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 862 | 0.76 | 0.80 | 82 | empty |
| 2 | 263 | 0.65 | 0.82 | 27 | empty |
| 3 | 252 | 0.54 | 0.77 | 31 | MN |
| 4 | 200 | 0.50 | 0.76 | 29 | MN |
| 5 | 86 | 0.33 | 0.74 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 871 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 4MR0 · Crystal structure of PfbA, a surface adhesin of Streptococcus pneumoniae · the same entry in another collection · chain A against A, TM-score 1.00
- Q8CYC9 · AlphaFold monomer V2.0 prediction for plasmin and fibronectin-binding protein a (Q8CYC9) · a predicted model of the same protein · chain A against A, TM-score 1.00
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 Q8CYC9
- Elsewhere: RCSB PDB 4MR0 · PDBe 4MR0 · UniProt Q8CYC9
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