MolNFT v1 · #101499 · protein
Crystal structure of an L,D-carboxypeptidase dacb from streptococcus pneumonia
4NT9 · Putative uncharacterized protein: “Crystal structure of an L,D-carboxypeptidase dacb from streptococcus pneumonia”. X-ray diffraction, 1 ligand (ZN), 10 pockets (best druggability 0.81). MolNFT v1 #101499 on GenesisL1: 3D structure…
- PDB
- 4NT9
- Type
- protein
- Length
- 552 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative uncharacterized protein
- UniProt
- Q97RZ7
- Ligands
- ZN
- Pockets
- 10 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A, C | Putative uncharacterized protein | protein | 184 | 41% helix, 16% strand | Q97RZ7 |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 copies · chains B, A, C
- GOL · Glycerol · additive · 4 copies · chains B, A, C
- ACT · Acetate ion · additive · 3 copies · chains B, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 858 | 0.81 | 0.83 | 65 | empty |
| 2 | 133 | 0.56 | 0.83 | 25 | empty |
| 3 | 96 | 0.51 | 0.82 | 23 | ACT |
| 4 | 56 | 0.49 | 0.86 | 18 | empty |
| 5 | 113 | 0.48 | 0.80 | 32 | ACT, GOL |
Interfaces
2 interfaces between chains.
- B–A · 675 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 358 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4NT9 · Crystal structure of an L,D-carboxypeptidase DacB from Streptococcus pneumonia · 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 Q97RZ7
- Elsewhere: RCSB PDB 4NT9 · PDBe 4NT9 · UniProt Q97RZ7
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