Research workbench
Crystal structure of a major outer membrane protein from thermus thermophilus HB27
Analyse Crystal structure of a major outer membrane protein from thermus thermophilus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DZM
- Type
- protein
- Length
- 614 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical conserved protein
- UniProt
- Q72JD8
- Ligands
- CA
- Pockets
- 11 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 62% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypothetical conserved protein | protein | 208 | 7% helix, 61% strand | Q72JD8 |
| B | Hypothetical conserved protein | protein | 204 | 7% helix, 62% strand | Q72JD8 |
| C | Hypothetical conserved protein | protein | 202 | 6% helix, 62% strand | Q72JD8 |
Ligands and binding sites
- CA · Calcium ion · metal · 3 copies · chains A, B, C
- C8E · (hydroxyethyloxy)tri(ethyloxy)octane · additive · 6 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 246 | 0.56 | 0.78 | 28 | empty |
| 2 | 159 | 0.45 | 0.75 | 28 | empty |
| 3 | 105 | 0.43 | 0.78 | 18 | empty |
| 4 | 89 | 0.43 | 0.78 | 15 | empty |
| 5 | 124 | 0.42 | 0.75 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–C · 850 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 573 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 82 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 3DZM · Crystal structure of a major outer membrane protein from Thermus thermophilus HB27 · 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 Q72JD8
- Elsewhere: RCSB PDB 3DZM · PDBe 3DZM · UniProt Q72JD8
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