Research workbench
Crystal Structure of Medicago truncatula Agmatine Iminohydrolase (Deiminase) in Complex with 6-aminohexanamide
Analyse Crystal Structure of Medicago truncatula Agmatine Iminohydrolase (Deiminase) in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NIC
- Type
- protein
- Length
- 1,430 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.2
- Source
- Medicago truncatula
- Molecule
- Porphyromonas-type peptidyl-arginine deiminase
- EC
- 3.5.3.12
- UniProt
- G7JT50
- Ligands
- KQY, NA
- Pockets
- 11 · best druggability 0.70
Structure
x-ray diffraction · resolution 2.2 · 3 distinct chains · 31% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Porphyromonas-type peptidyl-arginine deiminase (EC 3.5.3.12) | protein | 356 | 32% helix, 24% strand | G7JT50 |
| C | Porphyromonas-type peptidyl-arginine deiminase (EC 3.5.3.12) | protein | 358 | 31% helix, 25% strand | G7JT50 |
| D | Porphyromonas-type peptidyl-arginine deiminase (EC 3.5.3.12) | protein | 360 | 29% helix, 24% strand | G7JT50 |
Ligands and binding sites
- KQY · 6-aminohexanamide · ligand · 3 copies · chains A, C, D
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B
- PGE · Triethylene glycol · additive · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 192 | 0.70 | 0.87 | 32 | KQY |
| 2 | 71 | 0.70 | 0.95 | 22 | KQY |
| 3 | 467 | 0.62 | 0.76 | 49 | empty |
| 4 | 117 | 0.56 | 0.84 | 18 | empty |
| 5 | 91 | 0.53 | 0.85 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–B · 973 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 951 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 512 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6NIC · Crystal structure of medicago truncatula agmatine iminohydrolase (deiminase) in complex… · the same entry in another collection · chain D against D, TM-score 1.00
- G7JT50 · AlphaFold monomer V2.0 prediction for agmatine deiminase (G7JT50) · a predicted model of the same protein · chain B 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 G7JT50
- Elsewhere: RCSB PDB 6NIC · PDBe 6NIC · UniProt G7JT50
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.