MolNFT v1 · #15369 · protein
The S53A proenzyme structure of methanococcus jannaschii.
1N2M · Pyruvoyl-dependent arginine decarboxylase: “The S53A proenzyme structure of methanococcus jannaschii.”. X-ray diffraction, 4 pockets (best druggability 0.76). MolNFT v1 #15369 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1N2M
- Type
- protein
- Length
- 951 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvoyl-dependent arginine decarboxylase
- EC
- 4.1.1.19
- UniProt
- Q57764
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 6 distinct chains · 20% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyruvoyl-dependent arginine decarboxylase (EC 4.1.1.19) | protein | 159 | 19% helix, 44% strand | Q57764 |
| B | Pyruvoyl-dependent arginine decarboxylase (EC 4.1.1.19) | protein | 160 | 21% helix, 44% strand | Q57764 |
| C | Pyruvoyl-dependent arginine decarboxylase (EC 4.1.1.19) | protein | 163 | 19% helix, 43% strand | Q57764 |
| D | Pyruvoyl-dependent arginine decarboxylase (EC 4.1.1.19) | protein | 154 | 20% helix, 45% strand | Q57764 |
| E | Pyruvoyl-dependent arginine decarboxylase (EC 4.1.1.19) | protein | 162 | 19% helix, 43% strand | Q57764 |
| F | Pyruvoyl-dependent arginine decarboxylase (EC 4.1.1.19) | protein | 153 | 20% helix, 46% strand | Q57764 |
Ligands and binding sites
- MRD · (4R)-2-methylpentane-2,4-diol · additive · 8 copies · chains A, C, B, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 919 | 0.76 | 0.79 | 81 | empty |
| 2 | 582 | 0.69 | 0.78 | 57 | MRD |
| 3 | 574 | 0.69 | 0.78 | 57 | MRD |
| 4 | 127 | 0.40 | 0.75 | 16 | empty |
Interfaces
8 interfaces between chains.
- B–C · 1187 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 1131 Ų buried · 14 hydrogen bonds · protein-protein
- D–E · 1098 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 1094 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1065 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 1N2M · The S53A Proenzyme Structure of Methanococcus jannaschii. · the same entry in another collection · chain F against F, TM-score 1.00
- Q57764 · AlphaFold monomer V2.0 prediction for pyruvoyl-dependent arginine decarboxylase (Q57764) · a predicted model of the same protein · chain C 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 Q57764
- Elsewhere: RCSB PDB 1N2M · PDBe 1N2M · UniProt Q57764
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