MolNFT v1 · #145885 · protein
Crystal structure of E.COLI rpph-dapf complex
6D13 · Diaminopimelate epimerase: “Crystal structure of E.COLI rpph-dapf complex”. X-ray diffraction, 2 ligands (IOD, CL), 5 pockets (best druggability 0.66). MolNFT v1 #145885 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6D13
- Type
- protein
- Length
- 433 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
- B7MH73, B7MLH6
- Ligands
- IOD, CL
- Pockets
- 5 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 20% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Diaminopimelate epimerase (EC 5.1.1.7) | protein | 275 | 17% helix, 40% strand | B7MH73 |
| B | RNA pyrophosphohydrolase (EC 3.6.1.-) | protein | 158 | 25% helix, 31% strand | B7MLH6 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 241 | 0.66 | 0.84 | 39 | IOD |
| 2 | 120 | 0.56 | 0.84 | 23 | empty |
| 3 | 55 | 0.31 | 0.76 | 16 | empty |
| 4 | 77 | 0.30 | 0.73 | 22 | CL |
| 5 | 71 | 0.30 | 0.74 | 15 | IOD |
Interfaces
1 interface between chains.
- A–B · 715 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6D13 · Crystal structure of E.coli RppH-DapF complex · the same entry in another collection · chain A against A, TM-score 1.00
- B7MH73 · AlphaFold monomer V2.0 prediction for diaminopimelate epimerase (B7MH73) · a predicted model of the same protein · chain A against A, TM-score 0.99
- B7MLH6 · AlphaFold monomer V2.0 prediction for RNA pyrophosphohydrolase (B7MLH6) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 B7MH73
- Every structure of UniProt B7MLH6
- Elsewhere: RCSB PDB 6D13 · PDBe 6D13 · UniProt B7MH73 · UniProt B7MLH6
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