MolNFT v1 · #119616 · protein
Aspartate transcarbamoylase domain of human cad in apo form
5G1O · Cad protein: “Aspartate transcarbamoylase domain of human cad in apo form”. X-ray diffraction, 20 pockets (best druggability 0.83). MolNFT v1 #119616 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5G1O
- Type
- protein
- Length
- 1,772 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cad protein
- EC
- 3.5.2.3, 2.1.3.2
- UniProt
- P27708
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 6 distinct chains · 42% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cad protein (EC 3.5.2.3, 2.1.3.2) | protein | 294 | 40% helix, 15% strand | P27708 |
| B | Cad protein (EC 3.5.2.3, 2.1.3.2) | protein | 296 | 44% helix, 15% strand | P27708 |
| C | Cad protein (EC 3.5.2.3, 2.1.3.2) | protein | 290 | 42% helix, 14% strand | P27708 |
| D | Cad protein (EC 3.5.2.3, 2.1.3.2) | protein | 291 | 41% helix, 16% strand | P27708 |
| E | Cad protein (EC 3.5.2.3, 2.1.3.2) | protein | 300 | 42% helix, 15% strand | P27708 |
| F | Cad protein (EC 3.5.2.3, 2.1.3.2) | protein | 301 | 45% helix, 15% strand | P27708 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, C, B, E, F
- GOL · Glycerol · additive · 2 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1128 | 0.83 | 0.84 | 143 | EDO, GOL |
| 2 | 1166 | 0.82 | 0.84 | 131 | EDO, GOL |
| 3 | 434 | 0.68 | 0.80 | 42 | EDO |
| 4 | 322 | 0.66 | 0.81 | 43 | empty |
| 5 | 326 | 0.65 | 0.81 | 44 | empty |
Interfaces
7 interfaces between chains.
- C–E · 1068 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 879 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 859 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 853 Ų buried · 12 hydrogen bonds · protein-protein
- D–F · 845 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
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 P27708
- Elsewhere: RCSB PDB 5G1O · PDBe 5G1O · UniProt P27708
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