Research workbench
Crystal structure of apo psd from E. COLI (2.63 a)
Analyse Crystal structure of apo psd from E. COLI (2.63 a) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7CNX
- Type
- protein
- Length
- 1,126 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphatidylserine decarboxylase beta chain; Phosphatidylserine decarboxylase alpha chain
- EC
- 4.1.1.65
- UniProt
- A0A6D2XQZ0
- Ligands
- PYR
- Pockets
- 15 · best druggability 0.76
Structure
x-ray diffraction · 8 distinct chains · 22% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphatidylserine decarboxylase beta chain (EC 4.1.1.65) | protein | 246 | 25% helix, 33% strand | A0A6D2XQZ0 |
| B | Phosphatidylserine decarboxylase alpha chain (EC 4.1.1.65) | protein | 38 | 0% helix, 39% strand | A0A6D2XQZ0 |
| C | Phosphatidylserine decarboxylase beta chain (EC 4.1.1.65) | protein | 240 | 25% helix, 33% strand | A0A6D2XQZ0 |
| D | Phosphatidylserine decarboxylase alpha chain (EC 4.1.1.65) | protein | 33 | 0% helix, 45% strand | A0A6D2XQZ0 |
| E | Phosphatidylserine decarboxylase beta chain (EC 4.1.1.65) | protein | 249 | 27% helix, 32% strand | A0A6D2XQZ0 |
| F | Phosphatidylserine decarboxylase alpha chain (EC 4.1.1.65) | protein | 37 | 0% helix, 41% strand | A0A6D2XQZ0 |
| G | Phosphatidylserine decarboxylase beta chain (EC 4.1.1.65) | protein | 244 | 25% helix, 33% strand | A0A6D2XQZ0 |
| H | Phosphatidylserine decarboxylase alpha chain (EC 4.1.1.65) | protein | 39 | 0% helix, 38% strand | A0A6D2XQZ0 |
Ligands and binding sites
- PYR · Pyruvic acid · ligand · 4 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 680 | 0.76 | 0.82 | 53 | empty |
| 2 | 568 | 0.73 | 0.81 | 51 | empty |
| 3 | 58 | 0.70 | 0.97 | 18 | empty |
| 4 | 1008 | 0.70 | 0.74 | 91 | empty |
| 5 | 52 | 0.66 | 0.95 | 18 | empty |
Interfaces
11 interfaces between chains.
- A–B · 1872 Ų buried · 35 hydrogen bonds · protein-protein
- E–F · 1825 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 1821 Ų buried · 33 hydrogen bonds · protein-protein
- G–H · 1799 Ų buried · 32 hydrogen bonds · protein-protein
- A–C · 802 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 7CNX · Crystal structure of Apo PSD from E. coli (2.63 A) · 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 A0A6D2XQZ0
- Elsewhere: RCSB PDB 7CNX · PDBe 7CNX · UniProt A0A6D2XQZ0
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