MolNFT v1 · #71025 · protein
Crystal structure of a putative gamma-D-glutamyl-L-diamino acid endopeptidase (DVU_0896) from desulfovibrio vulgaris hildenborough at 1.75 a resolution
3M1U: “Crystal structure of a putative gamma-D-glutamyl-L-diamino acid endopeptidase (DVU_0896) from desulfovibrio…”. X-ray diffraction, 1 ligand (CL), 10 pockets (best druggability 0.86). MolNFT v1 #71025 on GenesisL1: 3D structure…
- PDB
- 3M1U
- Type
- protein
- Length
- 845 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative gamma-D-glutamyl-L-diamino acid endopeptidase
- UniProt
- Q72DN3
- Ligands
- CL
- Pockets
- 10 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative gamma-D-glutamyl-L-diamino acid endopeptidase | protein | 425 | 27% helix, 30% strand | Q72DN3 |
| B | Putative gamma-D-glutamyl-L-diamino acid endopeptidase | protein | 420 | 28% helix, 32% strand | Q72DN3 |
Ligands and binding sites
- CL · Chloride ion · ion · 9 copies · chains A, B
- GOL · Glycerol · additive · 11 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1128 | 0.86 | 0.87 | 113 | GOL |
| 2 | 54 | 0.71 | 0.99 | 22 | GOL |
| 3 | 51 | 0.69 | 0.98 | 19 | GOL |
| 4 | 551 | 0.64 | 0.75 | 51 | GOL, CL |
| 5 | 227 | 0.57 | 0.79 | 30 | GOL, ACT, MES |
Interfaces
1 interface between chains.
- A–B · 2093 Ų buried · 31 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 30 modified (engineered).
Compared structures
- 3M1U · Crystal structure of a Putative gamma-D-glutamyl-L-diamino acid endopeptidase (DVU_0896)… · the same entry in another collection · chain B against B, 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 Q72DN3
- Elsewhere: RCSB PDB 3M1U · PDBe 3M1U · UniProt Q72DN3
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