MolNFT v1 · #170530 · protein
Crystal structure of pnra from S. pneumoniae in complex with thymidine
6YAG · Lipoprotein: “Crystal structure of pnra from S. pneumoniae in complex with thymidine”. X-ray diffraction, 2 ligands (THM, NI), 9 pockets (best druggability 0.73). MolNFT v1 #170530 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6YAG
- Type
- protein
- Length
- 1,316 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lipoprotein
- UniProt
- A0A0H2UPF3
- Ligands
- THM, NI
- Pockets
- 9 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Lipoprotein | protein | 330 | 41% helix, 22% strand | A0A0H2UPF3 |
| A, B | Lipoprotein | protein | 329 | 40% helix, 22% strand | A0A0H2UPF3 |
| D | Lipoprotein | protein | 328 | 40% helix, 22% strand | A0A0H2UPF3 |
Ligands and binding sites
- THM · Thymidine · ligand · 4 copies · chains C, A, B, D
- NI · Nickel (II) ion · metal · 7 copies · chains C, A, B, D
- ACT · Acetate ion · additive · chains 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 73 | 0.73 | 0.97 | 22 | THM |
| 2 | 68 | 0.73 | 0.97 | 21 | THM |
| 3 | 68 | 0.73 | 0.97 | 23 | THM |
| 4 | 798 | 0.72 | 0.77 | 61 | empty |
| 5 | 69 | 0.72 | 0.96 | 23 | THM |
Interfaces
3 interfaces between chains.
- C–A · 681 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 224 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 192 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6YAG · Crystal structure of PnrA from S. pneumoniae in complex with thymidine · the same entry in another collection · chain C against C, 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 A0A0H2UPF3
- Elsewhere: RCSB PDB 6YAG · PDBe 6YAG · UniProt A0A0H2UPF3
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