MolNFT v1 · #120696 · protein
Crystal structure of medicago truncatula N-carbamoylputrescine amidohydrolase (mtcpa) in complex with N-(DIHYDROXYMETHYL)PUTRESCINE
5H8I: “Crystal structure of medicago truncatula N-carbamoylputrescine amidohydrolase (mtcpa) in complex with…”. X-ray diffraction, 2 ligands (N2H, NA), 20 pockets (best druggability 0.83). MolNFT v1 #120696 on GenesisL1: 3D structure…
- PDB
- 5H8I
- Type
- protein
- Length
- 4,736 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-carbamoylputrescine amidohydrolase
- EC
- 3.5.1.53
- UniProt
- G7ITU5
- Ligands
- N2H, NA
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 8 distinct chains · 31% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-carbamoylputrescine amidohydrolase (EC 3.5.1.53) | protein | 296 | 30% helix, 30% strand | G7ITU5 |
| B, D, F, J, L, N | N-carbamoylputrescine amidohydrolase (EC 3.5.1.53) | protein | 298 | 31% helix, 31% strand | G7ITU5 |
| C, K | N-carbamoylputrescine amidohydrolase (EC 3.5.1.53) | protein | 301 | 30% helix, 30% strand | G7ITU5 |
| E, M, O | N-carbamoylputrescine amidohydrolase (EC 3.5.1.53) | protein | 297 | 31% helix, 30% strand | G7ITU5 |
| G | N-carbamoylputrescine amidohydrolase (EC 3.5.1.53) | protein | 295 | 31% helix, 30% strand | G7ITU5 |
| H | N-carbamoylputrescine amidohydrolase (EC 3.5.1.53) | protein | 282 | 32% helix, 29% strand | G7ITU5 |
| I | N-carbamoylputrescine amidohydrolase (EC 3.5.1.53) | protein | 293 | 31% helix, 30% strand | G7ITU5 |
| P | N-carbamoylputrescine amidohydrolase (EC 3.5.1.53) | protein | 289 | 31% helix, 30% strand | G7ITU5 |
Ligands and binding sites
- N2H · (4-azanylbutylamino)methanediol · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
- NA · Sodium ion · metal · chains L
- GOL · Glycerol · additive · 35 copies · chains A, B, C, D, E, F, G, L, H, I, J, K, M, N, O, P
- PEG · Di(hydroxyethyl)ether · additive · 6 copies · chains A, D, G, J, L
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B, C, D, E, F, K, L, M, N, O, P
- PGE · Triethylene glycol · additive · 4 copies · chains A, B, C, G, I, J
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 | 194 | 0.83 | 0.97 | 38 | EDO, GOL |
| 2 | 201 | 0.83 | 0.97 | 38 | empty |
| 3 | 195 | 0.83 | 0.97 | 37 | EDO |
| 4 | 203 | 0.83 | 0.96 | 38 | GOL |
| 5 | 198 | 0.82 | 0.96 | 38 | EDO |
Interfaces
33 interfaces between chains.
- M–N · 2512 Ų buried · 39 hydrogen bonds · protein-protein
- K–L · 2497 Ų buried · 40 hydrogen bonds · protein-protein
- E–F · 2493 Ų buried · 40 hydrogen bonds · protein-protein
- C–D · 2483 Ų buried · 40 hydrogen bonds · protein-protein
- A–B · 2480 Ų buried · 35 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 covalent (covalent ligand).
Compared structures
- 5H8I · Crystal structure of Medicago truncatula N-carbamoylputrescine amidohydrolase (MtCPA) in… · 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 5H8I · PDBe 5H8I · UniProt G7ITU5
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