Research workbench
Protein CGD2_2020 from cryptosporidium parvum
Analyse Protein CGD2_2020 from cryptosporidium parvum in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PD0
- Type
- protein
- Length
- 818 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein
- UniProt
- Q5CTR0
- Pockets
- 14 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Hypothetical protein | protein | 205 | 28% helix, 25% strand | Q5CTR0 |
| D | Hypothetical protein | protein | 203 | 28% helix, 25% strand | Q5CTR0 |
Ligands and binding sites
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1179 | 0.84 | 0.85 | 107 | MES |
| 2 | 502 | 0.82 | 0.88 | 63 | MES |
| 3 | 624 | 0.81 | 0.86 | 66 | MES |
| 4 | 612 | 0.81 | 0.86 | 71 | MES |
| 5 | 75 | 0.73 | 0.96 | 22 | empty |
Interfaces
4 interfaces between chains.
- A–C · 1233 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 1119 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 531 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 26 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 2PD0 · Protein cgd2_2020 from Cryptosporidium parvum · 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 Q5CTR0
- Elsewhere: RCSB PDB 2PD0 · PDBe 2PD0 · UniProt Q5CTR0
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