Research workbench
Structure of carbamoyl phosphate synthetase complexed with the ATP analog amppnp
Analyse Structure of carbamoyl phosphate synthetase complexed with the ATP analog amppnp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1BXR
- Type
- protein
- Length
- 5,808 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carbamoyl-phosphate synthase
- EC
- 6.3.5.5
- UniProt
- P00968, P0A6F1
- Ligands
- ANP, ORN, NET, K, MN, CL
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Carbamoyl-phosphate synthase (EC 6.3.5.5) | protein | 1073 | 39% helix, 20% strand | P00968 |
| B, D, F, H | Carbamoyl-phosphate synthase (EC 6.3.5.5) | protein | 379 | 25% helix, 32% strand | P0A6F1 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 8 copies · chains A, C, E, G
- ORN · L-ornithine · ligand · 4 copies · chains A, C, E, G
- NET · Tetraethylammonium ion · ligand · 4 copies · chains A, C, E, G
- K · Potassium ion · metal · 19 copies · chains A, B, C, D, E, G, H
- MN · Manganese (II) ion · metal · 13 copies · chains A, C, E, G
- CL · Chloride ion · ion · 14 copies · chains A, B, C, D, E, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 198 | 0.82 | 0.96 | 37 | MN, ANP |
| 2 | 953 | 0.82 | 0.84 | 71 | CL, ORN, NET |
| 3 | 187 | 0.82 | 0.96 | 33 | MN, ANP |
| 4 | 187 | 0.82 | 0.97 | 39 | MN, ANP |
| 5 | 184 | 0.81 | 0.97 | 37 | MN, ANP |
Interfaces
8 interfaces between chains.
- A–B · 2467 Ų buried · 42 hydrogen bonds · protein-protein
- G–H · 2455 Ų buried · 36 hydrogen bonds · protein-protein
- E–F · 2450 Ų buried · 44 hydrogen bonds · protein-protein
- C–D · 2435 Ų buried · 40 hydrogen bonds · protein-protein
- A–G · 595 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 1BXR · Structure of carbamoyl phosphate synthetase complexed with the ATP analog amppnp · the same entry in another collection · chain D against D, TM-score 1.00
- P0A6F1 · AlphaFold monomer V2.0 prediction for carbamoyl-phosphate synthase small chain (P0A6F1) · a predicted model of the same protein · chain D 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 P00968
- Every structure of UniProt P0A6F1
- Elsewhere: RCSB PDB 1BXR · PDBe 1BXR · UniProt P00968 · UniProt P0A6F1
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