MolNFT v1 · #145908 · protein
Crystal structure of E. COLI rpph-dapf complex, monomer
6D1Q · Diaminopimelate epimerase: “Crystal structure of E. COLI rpph-dapf complex, monomer”. X-ray diffraction, 1 ligand (CL), 4 pockets (best druggability 0.55). MolNFT v1 #145908 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6D1Q
- Type
- protein
- Length
- 435 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Diaminopimelate epimerase; RNA pyrophosphohydrolase
- EC
- 5.1.1.7, 3.6.1.-
- UniProt
- P0A6K1, P0A776
- Ligands
- CL
- Pockets
- 4 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 19% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Diaminopimelate epimerase (EC 5.1.1.7) | protein | 275 | 15% helix, 41% strand | P0A6K1 |
| B | RNA pyrophosphohydrolase (EC 3.6.1.-) | protein | 160 | 27% helix, 31% strand | P0A776 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 242 | 0.55 | 0.78 | 32 | CL |
| 2 | 70 | 0.51 | 0.86 | 22 | empty |
| 3 | 108 | 0.37 | 0.74 | 24 | empty |
| 4 | 82 | 0.35 | 0.75 | 15 | CL |
Interfaces
1 interface between chains.
- A–B · 745 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6D1Q · Crystal structure of E. coli RppH-DapF complex, monomer · the same entry in another collection · chain A against A, TM-score 1.00
- P0A776 · AlphaFold monomer V2.0 prediction for RNA pyrophosphohydrolase (P0A776) · a predicted model of the same protein · chain B against A, TM-score 0.98
- P0A6K1 · AlphaFold monomer V2.0 prediction for diaminopimelate epimerase (P0A6K1) · a predicted model of the same protein · chain A against A, TM-score 0.89
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 P0A6K1
- Every structure of UniProt P0A776
- Elsewhere: RCSB PDB 6D1Q · PDBe 6D1Q · UniProt P0A6K1 · UniProt P0A776
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.