Research workbench
Crystal structure of the Q04L03_STRP2 protein from streptococcus pneumoniae. northeast structural genomics consortium target SPR105
Analyse Crystal structure of the Q04L03_STRP2 protein from streptococcus pneumoniae.… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RL6
- Type
- protein
- Length
- 810 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Saccharopine dehydrogenase
- EC
- 1.5.1.7
- UniProt
- Q04L03
- Ligands
- NDP
- Pockets
- 4 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Saccharopine dehydrogenase (EC 1.5.1.7) | protein | 414 | 38% helix, 27% strand | Q04L03 |
| B | Saccharopine dehydrogenase (EC 1.5.1.7) | protein | 396 | 38% helix, 26% strand | Q04L03 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1196 | 0.82 | 0.83 | 107 | NDP |
| 2 | 1052 | 0.78 | 0.80 | 84 | NDP |
| 3 | 59 | 0.35 | 0.78 | 15 | empty |
| 4 | 51 | 0.28 | 0.75 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 663 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 4RL6 · Crystal Structure of the Q04L03_STRP2 protein from Streptococcus pneumoniae. Northeast… · 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 Q04L03
- Elsewhere: RCSB PDB 4RL6 · PDBe 4RL6 · UniProt Q04L03
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