MolNFT v1 · #135317 · protein
Crystal structure of foldase protein prsa from streptococcus pneumoniae str. canada MDR_19A
5TVL: “Crystal structure of foldase protein prsa from streptococcus pneumoniae str. canada MDR_19A”. X-ray diffraction, 2 ligands (CL, SO4), 9 pockets (best druggability 0.77). MolNFT v1 #135317 on GenesisL1: 3D structure, binding sites…
- PDB
- 5TVL
- Type
- protein
- Length
- 1,068 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Foldase protein prsa
- EC
- 5.2.1.8
- UniProt
- B1IBE1
- Ligands
- CL, SO4
- Pockets
- 9 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 59% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Foldase protein prsa (EC 5.2.1.8) | protein | 270 | 59% helix, 14% strand | B1IBE1 |
| B | Foldase protein prsa (EC 5.2.1.8) | protein | 266 | 58% helix, 14% strand | B1IBE1 |
| C | Foldase protein prsa (EC 5.2.1.8) | protein | 266 | 58% helix, 12% strand | B1IBE1 |
| D | Foldase protein prsa (EC 5.2.1.8) | protein | 266 | 61% helix, 14% strand | B1IBE1 |
Ligands and binding sites
- CL · Chloride ion · ion · 7 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- GOL · Glycerol · additive · 7 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1152 | 0.77 | 0.79 | 101 | CL, GOL |
| 2 | 666 | 0.75 | 0.81 | 74 | SO4 |
| 3 | 417 | 0.61 | 0.76 | 44 | SO4 |
| 4 | 258 | 0.61 | 0.80 | 30 | empty |
| 5 | 199 | 0.57 | 0.80 | 24 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2191 Ų buried · 28 hydrogen bonds · protein-protein
- A–D · 2004 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 1945 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 381 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 313 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5TVL · Crystal structure of foldase protein PrsA from Streptococcus pneumoniae str. Canada… · the same entry in another collection · chain D against D, TM-score 1.00
- B1IBE1 · AlphaFold monomer V2.0 prediction for foldase protein prsa (B1IBE1) · a predicted model of the same protein · chain D 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 B1IBE1
- Elsewhere: RCSB PDB 5TVL · PDBe 5TVL · UniProt B1IBE1
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