Research workbench
1.8 ångström resolution crystal structure of diaminopimelate decarboxylase (lysa) from vibrio cholerae.
Analyse 1.8 ångström resolution crystal structure of diaminopimelate decarboxylase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3N2B
- Type
- protein
- Length
- 1,612 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Diaminopimelate decarboxylase
- EC
- 4.1.1.20
- UniProt
- Q9KVL7
- Ligands
- CL
- Pockets
- 20 · best druggability 0.61
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Diaminopimelate decarboxylase (EC 4.1.1.20) | protein | 411 | 33% helix, 27% strand | Q9KVL7 |
| B | Diaminopimelate decarboxylase (EC 4.1.1.20) | protein | 392 | 32% helix, 28% strand | Q9KVL7 |
| C | Diaminopimelate decarboxylase (EC 4.1.1.20) | protein | 411 | 34% helix, 26% strand | Q9KVL7 |
| D | Diaminopimelate decarboxylase (EC 4.1.1.20) | protein | 398 | 36% helix, 26% strand | Q9KVL7 |
Ligands and binding sites
- CL · Chloride ion · ion · 4 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, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 276 | 0.61 | 0.79 | 35 | CL |
| 2 | 254 | 0.59 | 0.79 | 34 | CL |
| 3 | 335 | 0.59 | 0.77 | 44 | empty |
| 4 | 272 | 0.57 | 0.77 | 38 | empty |
| 5 | 149 | 0.57 | 0.82 | 29 | empty |
Interfaces
3 interfaces between chains.
- C–D · 3710 Ų buried · 68 hydrogen bonds · protein-protein
- A–B · 3572 Ų buried · 62 hydrogen bonds · protein-protein
- A–C · 996 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 3N2B · 1.8 Angstrom Resolution Crystal Structure of Diaminopimelate Decarboxylase (lysA) from… · the same entry in another collection · chain D against D, TM-score 1.00
- Q9KVL7 · AlphaFold monomer V2.0 prediction for diaminopimelate decarboxylase (Q9KVL7) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 Q9KVL7
- Elsewhere: RCSB PDB 3N2B · PDBe 3N2B · UniProt Q9KVL7
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