Research workbench
Crystal structure of SMU.1420 from streptococcus mutans UA159
Analyse Crystal structure of SMU.1420 from streptococcus mutans UA159 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LCM
- Type
- protein
- Length
- 768 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative oxidoreductase
- EC
- 1.6.99.2
- UniProt
- Q8DTD1
- Ligands
- FAD, NAP
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Putative oxidoreductase (EC 1.6.99.2) | protein | 196 | 36% helix, 21% strand | Q8DTD1 |
| B, D | Putative oxidoreductase (EC 1.6.99.2) | protein | 188 | 37% helix, 22% strand | Q8DTD1 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 56 | 0.73 | 0.99 | 21 | empty |
| 2 | 53 | 0.72 | 0.99 | 16 | empty |
| 3 | 478 | 0.71 | 0.81 | 43 | NAP, FAD |
| 4 | 799 | 0.71 | 0.77 | 76 | empty |
| 5 | 504 | 0.71 | 0.80 | 40 | FAD, NAP |
Interfaces
3 interfaces between chains.
- A–B · 1580 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1564 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 429 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3LCM · Crystal structure of Smu.1420 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 Q8DTD1
- Elsewhere: RCSB PDB 3LCM · PDBe 3LCM · UniProt Q8DTD1
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