MolNFT v1 · #180656 · protein
Crystal structure of peptidyl-prolyl cis-trans isomerasefrom (ppib) streptococcus pneumoniae R6
7L6Z: “Crystal structure of peptidyl-prolyl cis-trans isomerasefrom (ppib) streptococcus pneumoniae R6”. X-ray diffraction, 1 ligand (CL), 20 pockets (best druggability 0.78). MolNFT v1 #180656 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7L6Z
- Type
- protein
- Length
- 2,132 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidyl-prolyl cis-trans isomerase
- EC
- 5.2.1.8
- UniProt
- Q8DQG5
- Ligands
- CL
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 17% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Peptidyl-prolyl cis-trans isomerase (EC 5.2.1.8) | protein | 214 | 18% helix, 24% strand | Q8DQG5 |
| B, C, E, F, G, H, I, J | Peptidyl-prolyl cis-trans isomerase (EC 5.2.1.8) | protein | 213 | 17% helix, 24% strand | Q8DQG5 |
Ligands and binding sites
- CL · Chloride ion · ion · 7 copies · chains A, B, D, E, G
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 8 copies · chains B, C, D, E, A, F, H, J
- EDO · 1,2-ethanediol · additive · 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 873 | 0.78 | 0.81 | 83 | empty |
| 2 | 507 | 0.77 | 0.85 | 62 | empty |
| 3 | 647 | 0.74 | 0.81 | 75 | MES |
| 4 | 309 | 0.63 | 0.80 | 43 | CL |
| 5 | 230 | 0.61 | 0.81 | 30 | CL |
Interfaces
19 interfaces between chains.
- B–C · 717 Ų buried · 9 hydrogen bonds · protein-protein
- A–F · 715 Ų buried · 8 hydrogen bonds · protein-protein
- B–I · 682 Ų buried · 9 hydrogen bonds · protein-protein
- C–F · 601 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 513 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 40 modified (engineered).
Compared structures
- 7L6Z · Crystal Structure of Peptidyl-Prolyl Cis-Trans Isomerasefrom (PpiB) Streptococcus… · the same entry in another collection · 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 Q8DQG5
- Elsewhere: RCSB PDB 7L6Z · PDBe 7L6Z · UniProt Q8DQG5
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