MolNFT v1 · #70183 · protein
The crystal structure of SMU.2055 from streptococcus mutans UA159
3LD2 · Putative acetyltransferase: “The crystal structure of SMU.2055 from streptococcus mutans UA159”. X-ray diffraction, 1 ligand (COA), 6 pockets (best druggability 0.76). MolNFT v1 #70183 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3LD2
- Type
- protein
- Length
- 638 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative acetyltransferase
- UniProt
- Q8DRZ8
- Ligands
- COA
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Putative acetyltransferase | protein | 159 | 31% helix, 37% strand | Q8DRZ8 |
| B | Putative acetyltransferase | protein | 162 | 32% helix, 37% strand | Q8DRZ8 |
| C | Putative acetyltransferase | protein | 158 | 33% helix, 37% strand | Q8DRZ8 |
Ligands and binding sites
- COA · Coenzyme A · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 957 | 0.76 | 0.78 | 72 | COA |
| 2 | 722 | 0.75 | 0.80 | 65 | COA |
| 3 | 678 | 0.75 | 0.81 | 62 | COA |
| 4 | 518 | 0.68 | 0.78 | 48 | COA |
| 5 | 87 | 0.45 | 0.81 | 15 | empty |
Interfaces
4 interfaces between chains.
- B–D · 974 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 757 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 183 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 55 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 3LD2 · The Crystal Structure of smu.2055 from Streptococcus mutans UA159 · the same entry in another collection · chain A against A, 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 Q8DRZ8
- Elsewhere: RCSB PDB 3LD2 · PDBe 3LD2 · UniProt Q8DRZ8
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