Research workbench
Crystal structure of the apo-form glycosyltransferase glye in streptococcus pneumoniae TIGR4
Analyse Crystal structure of the apo-form glycosyltransferase glye in streptococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5GVW
- Type
- protein
- Length
- 1,559 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycosyl transferase family 8
- UniProt
- A0A0Y1PI62
- Ligands
- MN
- Pockets
- 13 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Glycosyl transferase family 8 | protein | 391 | 38% helix, 20% strand | A0A0Y1PI62 |
| A | Glycosyl transferase family 8 | protein | 390 | 38% helix, 19% strand | A0A0Y1PI62 |
| B | Glycosyl transferase family 8 | protein | 389 | 38% helix, 19% strand | A0A0Y1PI62 |
| D | Glycosyl transferase family 8 | protein | 389 | 38% helix, 18% strand | A0A0Y1PI62 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 4 copies · chains C, A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 193 | 0.83 | 0.97 | 29 | empty |
| 2 | 180 | 0.82 | 0.97 | 30 | empty |
| 3 | 566 | 0.66 | 0.77 | 60 | empty |
| 4 | 551 | 0.65 | 0.76 | 56 | empty |
| 5 | 612 | 0.65 | 0.75 | 55 | empty |
Interfaces
3 interfaces between chains.
- C–D · 2040 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 2025 Ų buried · 19 hydrogen bonds · protein-protein
- C–B · 95 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5GVW · Crystal structure of the apo-form glycosyltransferase GlyE in Streptococcus pneumoniae… · the same entry in another collection · chain C against C, 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 A0A0Y1PI62
- Elsewhere: RCSB PDB 5GVW · PDBe 5GVW · UniProt A0A0Y1PI62
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