MolNFT v1 · #156113 · protein
Crystal structure of pyrrolidone carboxyl peptidase from thermophilic keratin degrading bacterium fervidobacterium islandicum aw-1 (fipcp)
6LTQ · Pyroglutamyl-peptidase I: “Crystal structure of pyrrolidone carboxyl peptidase from thermophilic keratin degrading bacterium…”. X-ray diffraction, 9 pockets (best druggability 0.69). MolNFT v1 #156113 on GenesisL1: 3D structure…
- PDB
- 6LTQ
- Type
- protein
- Length
- 842 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyroglutamyl-peptidase I
- EC
- 3.4.19.3
- UniProt
- A0A1B0VKK9
- Pockets
- 9 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyroglutamyl-peptidase I (EC 3.4.19.3) | protein | 210 | 35% helix, 25% strand | A0A1B0VKK9 |
| B | Pyroglutamyl-peptidase I (EC 3.4.19.3) | protein | 209 | 36% helix, 23% strand | A0A1B0VKK9 |
| C | Pyroglutamyl-peptidase I (EC 3.4.19.3) | protein | 208 | 36% helix, 23% strand | A0A1B0VKK9 |
| D | Pyroglutamyl-peptidase I (EC 3.4.19.3) | protein | 215 | 35% helix, 22% strand | A0A1B0VKK9 |
Ligands and binding sites
- GOL · Glycerol · additive · 18 copies · chains A, C, B, D
- 1PE · Pentaethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 446 | 0.69 | 0.80 | 38 | GOL |
| 2 | 631 | 0.68 | 0.77 | 45 | GOL |
| 3 | 489 | 0.66 | 0.78 | 38 | GOL |
| 4 | 352 | 0.65 | 0.80 | 34 | GOL |
| 5 | 71 | 0.35 | 0.76 | 15 | empty |
Interfaces
6 interfaces between chains.
- C–D · 879 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 849 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 739 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 724 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 111 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (oxidation).
Compared structures
- 6LTQ · Crystal structure of pyrrolidone carboxyl peptidase from thermophilic keratin degrading… · 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 A0A1B0VKK9
- Elsewhere: RCSB PDB 6LTQ · PDBe 6LTQ · UniProt A0A1B0VKK9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.