Research workbench
Crystal structure of putrescine transcarbamylase from enterococcus faecalis with N5-(phosphonoacetyl)-L-ornithine
Analyse Crystal structure of putrescine transcarbamylase from enterococcus faecalis… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4A8P
- Type
- protein
- Length
- 2,006 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putrescine carbamoyltransferase
- EC
- 2.1.3.6
- UniProt
- Q837U7
- Ligands
- PAO, NI
- Pockets
- 19 · best druggability 0.77
Structure
x-ray diffraction · 5 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Putrescine carbamoyltransferase (EC 2.1.3.6) | protein | 339 | 47% helix, 16% strand | Q837U7 |
| B | Putrescine carbamoyltransferase (EC 2.1.3.6) | protein | 338 | 47% helix, 15% strand | Q837U7 |
| D | Putrescine carbamoyltransferase (EC 2.1.3.6) | protein | 334 | 49% helix, 14% strand | Q837U7 |
| E | Putrescine carbamoyltransferase (EC 2.1.3.6) | protein | 333 | 48% helix, 15% strand | Q837U7 |
| F | Putrescine carbamoyltransferase (EC 2.1.3.6) | protein | 323 | 51% helix, 15% strand | Q837U7 |
Ligands and binding sites
- PAO · N-(phosphonoacetyl)-L-ornithine · ligand · 6 copies · chains A, B, C, D, E, F
- NI · Nickel (II) ion · metal · 2 copies · chains A, B, C, D, E, F
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 178 | 0.77 | 0.93 | 32 | PAO |
| 2 | 1022 | 0.76 | 0.78 | 93 | PAO |
| 3 | 255 | 0.73 | 0.88 | 39 | PAO, TRS |
| 4 | 259 | 0.72 | 0.87 | 41 | PAO, TRS |
| 5 | 69 | 0.71 | 0.97 | 23 | NI |
Interfaces
9 interfaces between chains.
- A–B · 2077 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 2068 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 2018 Ų buried · 28 hydrogen bonds · protein-protein
- D–E · 1982 Ų buried · 24 hydrogen bonds · protein-protein
- E–F · 1779 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 4A8P · Crystal structure of putrescine transcarbamylase from Enterococcus faecalis with… · the same entry in another collection · chain E against E, TM-score 1.00
- Q837U7 · AlphaFold monomer V2.0 prediction for putrescine carbamoyltransferase (Q837U7) · a predicted model of the same protein · chain E against A, TM-score 0.99
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 Q837U7
- Elsewhere: RCSB PDB 4A8P · PDBe 4A8P · UniProt Q837U7
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