MolNFT v1 · #140177 · protein
Crystal structure of H. pylori htra
5Y2D · Periplasmic serine endoprotease degp-like: “Crystal structure of H. pylori htra”. X-ray diffraction, 1 pocket (best druggability 0.67). MolNFT v1 #140177 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5Y2D
- Type
- protein
- Length
- 297 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Periplasmic serine endoprotease degp-like; Unk-unk-unk; Unk-unk-unk-unk-unk…
- EC
- 3.4.21.107
- UniProt
- G2J5T2
- Pockets
- 1 · best druggability 0.67
Structure
x-ray diffraction · 6 distinct chains · 10% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Periplasmic serine endoprotease degp-like (EC 3.4.21.107) | protein | 260 | 11% helix, 29% strand | G2J5T2 |
| B | Unk-unk-unk | protein | 3 | 0% helix, 0% strand | — |
| C | Unk-unk-unk-unk-unk | protein | 5 | 0% helix, 0% strand | — |
| D | Unk-unk-K-unk-unk-unk-unk-unk-unk-unk | protein | 10 | 0% helix, 0% strand | — |
| E | Unk-unk-unk-unk-unk-unk-unk-unk | protein | 8 | 0% helix, 0% strand | — |
| F | Unk-unk-unk-unk-unk-unk-unk-unk-unk-unk-unk | protein | 11 | 0% helix, 0% strand | — |
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 560 | 0.67 | 0.77 | 73 | empty |
Interfaces
6 interfaces between chains.
- A–B · 164 Ų buried · 2 hydrogen bonds · protein-protein
- C–F · 147 Ų buried · 4 hydrogen bonds · protein-protein
- D–E · 94 Ų buried · 0 hydrogen bonds · protein-protein
- D–F · 77 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 45 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5Y2D · Crystal structure of H. pylori HtrA · 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 G2J5T2
- Elsewhere: RCSB PDB 5Y2D · PDBe 5Y2D · UniProt G2J5T2
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