Research workbench
Crystal structure of medicago truncatula N-carbamoylputrescine amidohydrolase (mtcpa) C158S mutant in complex with putrescine
Analyse Crystal structure of medicago truncatula N-carbamoylputrescine amidohydrolase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5H8L
- Type
- protein
- Length
- 4,732 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-carbamoylputrescine amidohydrolase
- UniProt
- G7ITU5
- Ligands
- PUT
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 8 distinct chains · 30% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-carbamoylputrescine amidohydrolase | protein | 295 | 31% helix, 31% strand | G7ITU5 |
| B, D, F, J, L, N | N-carbamoylputrescine amidohydrolase | protein | 298 | 29% helix, 30% strand | G7ITU5 |
| C, K | N-carbamoylputrescine amidohydrolase | protein | 301 | 30% helix, 30% strand | G7ITU5 |
| E, M, O | N-carbamoylputrescine amidohydrolase | protein | 297 | 31% helix, 30% strand | G7ITU5 |
| G | N-carbamoylputrescine amidohydrolase | protein | 295 | 29% helix, 31% strand | G7ITU5 |
| H | N-carbamoylputrescine amidohydrolase | protein | 282 | 32% helix, 28% strand | G7ITU5 |
| I | N-carbamoylputrescine amidohydrolase | protein | 292 | 31% helix, 29% strand | G7ITU5 |
| P | N-carbamoylputrescine amidohydrolase | protein | 287 | 30% helix, 30% strand | G7ITU5 |
Ligands and binding sites
- PUT · 1,4-diaminobutane · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
- GOL · Glycerol · additive · 30 copies · chains A, B, C, D, E, F, G, H, L, I, J, K, M, N, O, P
- EDO · 1,2-ethanediol · additive · 17 copies · chains A, B, C, D, E, F, I, J, K, L, M, N, O, P
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains D, K, L
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 | 204 | 0.83 | 0.97 | 38 | EDO |
| 2 | 205 | 0.83 | 0.96 | 37 | EDO |
| 3 | 206 | 0.83 | 0.96 | 38 | EDO |
| 4 | 199 | 0.83 | 0.97 | 37 | EDO |
| 5 | 186 | 0.82 | 0.97 | 38 | empty |
Interfaces
33 interfaces between chains.
- M–N · 2502 Ų buried · 39 hydrogen bonds · protein-protein
- K–L · 2491 Ų buried · 40 hydrogen bonds · protein-protein
- C–D · 2489 Ų buried · 40 hydrogen bonds · protein-protein
- E–F · 2481 Ų buried · 41 hydrogen bonds · protein-protein
- A–B · 2477 Ų buried · 37 hydrogen bonds · protein-protein
Compared structures
- 5H8L · Crystal structure of Medicago truncatula N-carbamoylputrescine amidohydrolase (MtCPA)… · the same entry in another collection · chain A 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 G7ITU5
- Elsewhere: RCSB PDB 5H8L · PDBe 5H8L · UniProt G7ITU5
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