Research workbench
Crystal structure of a conserved domain protein (SP_1775) from streptococcus pneumoniae TIGR4 at 1.91 a resolution
Analyse Crystal structure of a conserved domain protein (SP_1775) from streptococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4IAJ
- Type
- protein
- Length
- 596 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Conserved domain protein
- UniProt
- Q97P69
- Ligands
- UNL, MG, UNX
- Pockets
- 6 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 29% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Conserved domain protein | protein | 76 | 30% helix, 34% strand | Q97P69 |
| B | Conserved domain protein | protein | 77 | 30% helix, 35% strand | Q97P69 |
| C, H | Conserved domain protein | protein | 75 | 31% helix, 35% strand | Q97P69 |
| D | Conserved domain protein | protein | 74 | 27% helix, 36% strand | Q97P69 |
| E, F, G | Conserved domain protein | protein | 73 | 27% helix, 36% strand | Q97P69 |
Ligands and binding sites
- UNL · Unknown ligand · ligand · 9 copies · chains A, D, B, E, F, C, G, H
- MG · Magnesium ion · metal · 3 copies · chains D, H, G, B, E
- UNX · Unknown atom or ion · ion · 5 copies · chains A, G
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, G, D, B, E, F, C, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 281 | 0.83 | 0.93 | 53 | EDO, MG |
| 2 | 292 | 0.83 | 0.93 | 49 | MG, EDO |
| 3 | 1067 | 0.82 | 0.82 | 74 | UNL, UNX |
| 4 | 263 | 0.81 | 0.93 | 48 | empty |
| 5 | 228 | 0.81 | 0.94 | 36 | EDO |
Interfaces
16 interfaces between chains.
- A–G · 600 Ų buried · 3 hydrogen bonds · protein-protein
- B–E · 553 Ų buried · 2 hydrogen bonds · protein-protein
- C–F · 550 Ų buried · 1 hydrogen bond · protein-protein
- D–H · 544 Ų buried · 1 hydrogen bond · protein-protein
- E–F · 355 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified, 4 disulfide (engineered, disulfide).
Compared structures
- 4IAJ · Crystal structure of a conserved domain protein (SP_1775) from Streptococcus pneumoniae… · the same entry in another collection · chain E against E, 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 Q97P69
- Elsewhere: RCSB PDB 4IAJ · PDBe 4IAJ · UniProt Q97P69
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