Research workbench
Crystal structure of B. fragilis N-succinylornithine transcarbamylase P90E mutant complexed with carbamoyl phosphate and N-acetylnorvaline
Analyse Crystal structure of B. fragilis N-succinylornithine transcarbamylase P90E… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2G7M
- 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.-
- Ligands
- AN0, CP, SO4
- Pockets
- 17 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| X, Y | Putative ornithine carbamoyltransferase (EC 2.1.3.-) | protein | 321 | 38% helix, 15% strand | — |
| Z, C, D, E | Putative ornithine carbamoyltransferase (EC 2.1.3.-) | protein | 320 | 38% helix, 15% strand | — |
Ligands and binding sites
- AN0 · N-acetyl-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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 906 | 0.87 | 0.89 | 51 | SO4 |
| 2 | 921 | 0.87 | 0.88 | 53 | SO4 |
| 3 | 145 | 0.71 | 0.91 | 34 | AN0, CP |
| 4 | 145 | 0.71 | 0.91 | 34 | AN0, CP |
| 5 | 144 | 0.71 | 0.90 | 35 | AN0, CP |
Interfaces
10 interfaces between chains.
- X–Y · 1509 Ų buried · 30 hydrogen bonds · protein-protein
- Y–Z · 1505 Ų buried · 29 hydrogen bonds · protein-protein
- D–E · 1505 Ų buried · 31 hydrogen bonds · protein-protein
- C–E · 1503 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 1492 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 2G7M · Crystal structure of B. fragilis N-succinylornithine transcarbamylase P90E mutant… · 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
- Elsewhere: RCSB PDB 2G7M · PDBe 2G7M
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