MolNFT v1 · #34801 · protein
Crystal structure of the PH0078 protein from pyrococcus horikoshii OT3
2DRH · 361AA long hypothetical D-aminopeptidase: “Crystal structure of the PH0078 protein from pyrococcus horikoshii OT3”. X-ray diffraction, 1 ligand (CL), 7 pockets (best druggability 0.86). MolNFT v1 #34801 on GenesisL1: 3D structure…
- PDB
- 2DRH
- Type
- protein
- Length
- 1,413 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 361AA long hypothetical D-aminopeptidase
- UniProt
- O57784
- Ligands
- CL
- Pockets
- 7 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 361AA long hypothetical D-aminopeptidase | protein | 354 | 30% helix, 30% strand | O57784 |
| B, C | 361AA long hypothetical D-aminopeptidase | protein | 353 | 31% helix, 30% strand | O57784 |
| D | 361AA long hypothetical D-aminopeptidase | protein | 353 | 31% helix, 30% strand | O57784 |
Ligands and binding sites
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 990 | 0.86 | 0.86 | 59 | empty |
| 2 | 1005 | 0.80 | 0.81 | 119 | CL |
| 3 | 637 | 0.73 | 0.80 | 62 | CL |
| 4 | 630 | 0.72 | 0.80 | 64 | CL |
| 5 | 604 | 0.72 | 0.80 | 66 | CL |
Interfaces
6 interfaces between chains.
- B–C · 1913 Ų buried · 29 hydrogen bonds · protein-protein
- A–D · 1901 Ų buried · 31 hydrogen bonds · protein-protein
- B–D · 1455 Ų buried · 34 hydrogen bonds · protein-protein
- A–C · 1435 Ų buried · 36 hydrogen bonds · protein-protein
- C–D · 1120 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 2DRH · Crystal structure of the PH0078 protein from Pyrococcus horikoshii OT3 · 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 O57784
- Elsewhere: RCSB PDB 2DRH · PDBe 2DRH · UniProt O57784
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