MolNFT v1 · #158042 · protein
Crystal structure of medicago truncatula agmatine iminohydrolase (deiminase)
6NIB · Porphyromonas-type peptidyl-arginine deiminase: “Crystal structure of medicago truncatula agmatine iminohydrolase (deiminase)”. X-ray diffraction, 1 ligand (NA), 1 pocket (best druggability 0.59). MolNFT v1 #158042 on GenesisL1: 3D…
- PDB
- 6NIB
- Type
- protein
- Length
- 345 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Porphyromonas-type peptidyl-arginine deiminase
- EC
- 3.5.3.12
- UniProt
- G7JT50
- Ligands
- NA
- Pockets
- 1 · best druggability 0.59
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Porphyromonas-type peptidyl-arginine deiminase (EC 3.5.3.12) | protein | 345 | 31% helix, 25% strand | G7JT50 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A
- GOL · Glycerol · additive · 3 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 270 | 0.59 | 0.79 | 36 | PEG |
Compared structures
- 6NIB · Crystal Structure of Medicago truncatula Agmatine Iminohydrolase (Deiminase) · the same entry in another collection · chain A against A, TM-score 1.00
- G7JT50 · AlphaFold monomer V2.0 prediction for agmatine deiminase (G7JT50) · a predicted model of the same protein · chain A 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 G7JT50
- Elsewhere: RCSB PDB 6NIB · PDBe 6NIB · UniProt G7JT50
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