MolNFT v1 · #109889 · protein
Psychromonas ingrahamii diaminopimelate decarboxylase with llp
4XG1: “Psychromonas ingrahamii diaminopimelate decarboxylase with llp”. X-ray diffraction, 4 ligands (TME, LLP, K), 20 pockets (best druggability 0.82). MolNFT v1 #109889 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4XG1
- Type
- protein
- Length
- 1,625 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Diaminopimelate decarboxylase
- EC
- 4.1.1.20
- UniProt
- A1SR00
- Ligands
- TME, LLP, K, SCN
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Diaminopimelate decarboxylase (EC 4.1.1.20) | protein | 393 | 32% helix, 27% strand | A1SR00 |
| B | Diaminopimelate decarboxylase (EC 4.1.1.20) | protein | 418 | 34% helix, 27% strand | A1SR00 |
| C | Diaminopimelate decarboxylase (EC 4.1.1.20) | protein | 411 | 32% helix, 27% strand | A1SR00 |
| D | Diaminopimelate decarboxylase (EC 4.1.1.20) | protein | 403 | 33% helix, 28% strand | A1SR00 |
Ligands and binding sites
- TME · Propane · ligand · 5 copies · chains A, B, D
- LLP · (2S)-2-amino-6-[[3-hydroxy-2-methyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]hexanoic acid · ligand · 4 copies · chains A, B, C, D
- K · Potassium ion · metal · 6 copies · chains A, D, B, C
- SCN · Thiocyanate ion · ion · 9 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 214 | 0.82 | 0.96 | 54 | empty |
| 2 | 81 | 0.74 | 0.98 | 21 | empty |
| 3 | 73 | 0.72 | 0.97 | 21 | empty |
| 4 | 75 | 0.71 | 0.97 | 22 | SCN, K |
| 5 | 402 | 0.71 | 0.83 | 65 | LLP, SCN |
Interfaces
6 interfaces between chains.
- A–B · 3847 Ų buried · 66 hydrogen bonds · protein-protein
- C–D · 3840 Ų buried · 68 hydrogen bonds · protein-protein
- B–D · 670 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 554 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 448 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4XG1 · Psychromonas ingrahamii diaminopimelate decarboxylase with LLP · 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 A1SR00
- Elsewhere: RCSB PDB 4XG1 · PDBe 4XG1 · UniProt A1SR00
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