Research workbench
Structure of Tannerella forsythia selenomethionine-derivatized potempin D mutant I53M
Analyse Structure of Tannerella forsythia selenomethionine-derivatized potempin D… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8EHB
- Type
- protein
- Length
- 599 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.4
- Source
- Tannerella forsythia (strain ATCC 43037 / JCM 10827 / CCUG 21028 A / KCTC 5666…
- Molecule
- Putative lipoprotein
- UniProt
- G8ULV2
- Pockets
- 12 · best druggability 0.65
Structure
x-ray diffraction · resolution 2.4 · 4 distinct chains · 9% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Putative lipoprotein | protein | 102 | 9% helix, 49% strand | G8ULV2 |
| B, D | Putative lipoprotein | protein | 100 | 9% helix, 46% strand | G8ULV2 |
| E | Putative lipoprotein | protein | 97 | 10% helix, 51% strand | G8ULV2 |
| F | Putative lipoprotein | protein | 98 | 9% helix, 50% strand | G8ULV2 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 519 | 0.65 | 0.77 | 51 | empty |
| 2 | 231 | 0.56 | 0.78 | 37 | empty |
| 3 | 235 | 0.55 | 0.77 | 35 | empty |
| 4 | 153 | 0.54 | 0.80 | 26 | empty |
| 5 | 237 | 0.52 | 0.76 | 27 | empty |
Interfaces
9 interfaces between chains.
- A–B · 1030 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 961 Ų buried · 12 hydrogen bonds · protein-protein
- B–E · 637 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 604 Ų buried · 2 hydrogen bonds · protein-protein
- E–F · 430 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 disulfide, 6 modified (disulfide, engineered).
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 G8ULV2
- Elsewhere: RCSB PDB 8EHB · PDBe 8EHB · UniProt G8ULV2
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