Research workbench
N-succinyl-L-ornithine transcarbamylase from B. fragilis complexed with carbamoyl phosphate and N-succinyl-L-norvaline
Analyse N-succinyl-L-ornithine transcarbamylase from B. fragilis complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2FG7
- Type
- protein
- Length
- 1,922 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative ornithine carbamoyltransferase
- EC
- 2.1.3.-
- UniProt
- Q5LI27
- Ligands
- SN0, CP, SO4
- Pockets
- 17 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| X, Y | Putative ornithine carbamoyltransferase (EC 2.1.3.-) | protein | 321 | 39% helix, 16% strand | Q5LI27 |
| Z, C, D, E | Putative ornithine carbamoyltransferase (EC 2.1.3.-) | protein | 320 | 39% helix, 16% strand | Q5LI27 |
Ligands and binding sites
- SN0 · N-(3-carboxypropanoyl)-L-norvaline · ligand · 6 copies · chains X, Z, Y, C, E, D
- CP · Phosphoric acid mono(formamide)ester · ligand · 6 copies · chains X, Z, Y, C, E, D
- SO4 · Sulfate ion · ion · 2 copies · chains X, Y, Z, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 952 | 0.87 | 0.88 | 55 | SO4 |
| 2 | 952 | 0.86 | 0.88 | 54 | SO4 |
| 3 | 190 | 0.70 | 0.88 | 35 | SN0, CP |
| 4 | 180 | 0.70 | 0.88 | 34 | SN0, CP |
| 5 | 182 | 0.70 | 0.87 | 33 | SN0, CP |
Interfaces
10 interfaces between chains.
- Y–Z · 1489 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1483 Ų buried · 23 hydrogen bonds · protein-protein
- X–Y · 1478 Ų buried · 21 hydrogen bonds · protein-protein
- C–E · 1478 Ų buried · 21 hydrogen bonds · protein-protein
- D–E · 1471 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 2FG7 · N-succinyl-L-ornithine transcarbamylase from B. fragilis complexed with carbamoyl… · the same entry in another collection · chain X against X, 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 Q5LI27
- Elsewhere: RCSB PDB 2FG7 · PDBe 2FG7 · UniProt Q5LI27
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