MolNFT v1 · #119617 · protein
Aspartate transcarbamoylase domain of human cad bound to carbamoyl phosphate
5G1P · Cad protein: “Aspartate transcarbamoylase domain of human cad bound to carbamoyl phosphate”. X-ray diffraction, 1 ligand (CP), 20 pockets (best druggability 0.85). MolNFT v1 #119617 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5G1P
- Type
- protein
- Length
- 1,763 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cad protein
- EC
- 2.1.3.2
- UniProt
- P27708
- Ligands
- CP
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 6 distinct chains · 41% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cad protein (EC 2.1.3.2) | protein | 292 | 41% helix, 14% strand | P27708 |
| B | Cad protein (EC 2.1.3.2) | protein | 288 | 41% helix, 15% strand | P27708 |
| C | Cad protein (EC 2.1.3.2) | protein | 288 | 41% helix, 15% strand | P27708 |
| D | Cad protein (EC 2.1.3.2) | protein | 292 | 41% helix, 14% strand | P27708 |
| E | Cad protein (EC 2.1.3.2) | protein | 299 | 41% helix, 14% strand | P27708 |
| F | Cad protein (EC 2.1.3.2) | protein | 304 | 42% helix, 12% strand | P27708 |
Ligands and binding sites
- CP · Phosphoric acid mono(formamide)ester · ligand · 6 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1150 | 0.85 | 0.87 | 114 | empty |
| 2 | 1184 | 0.85 | 0.86 | 117 | empty |
| 3 | 348 | 0.70 | 0.83 | 40 | CP |
| 4 | 546 | 0.69 | 0.79 | 60 | empty |
| 5 | 410 | 0.69 | 0.81 | 38 | CP |
Interfaces
9 interfaces between chains.
- D–E · 1085 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 1043 Ų buried · 13 hydrogen bonds · protein-protein
- C–E · 1030 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1020 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 1018 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- P27708 · AlphaFold monomer V2.0 prediction for cad protein (P27708) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 5G1P · PDBe 5G1P · UniProt P27708
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