Research workbench
Teg 12 ternary structure complexed with pap and the teicoplanin aglycone
Analyse Teg 12 ternary structure complexed with pap and the teicoplanin aglycone in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MGB
- Type
- protein
- Length
- 564 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TEG12; Teicoplanin aglycone
- EC
- 2.8.2.-
- UniProt
- B7T1D7
- Ligands
- PAP, CL
- Pockets
- 3 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TEG12 (EC 2.8.2.-) | protein | 286 | 45% helix, 11% strand | B7T1D7 |
| B | TEG12 (EC 2.8.2.-) | protein | 264 | 49% helix, 11% strand | B7T1D7 |
| C, D | Teicoplanin aglycone | protein | 7 | 0% helix, 0% strand | — |
Ligands and binding sites
- PAP · 3'-phosphate-adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A, D
- ACT · Acetate ion · additive · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 521 | 0.75 | 0.83 | 64 | PAP |
| 2 | 396 | 0.71 | 0.82 | 49 | PAP |
| 3 | 111 | 0.42 | 0.77 | 20 | empty |
Interfaces
4 interfaces between chains.
- A–C · 660 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 600 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 501 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 142 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 modified (nonstandard).
Compared structures
- 3MGB · Teg 12 Ternary Structure Complexed with PAP and the Teicoplanin Aglycone · 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 B7T1D7
- Elsewhere: RCSB PDB 3MGB · PDBe 3MGB · UniProt B7T1D7
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