Research workbench
Crystal structure of the fimbrial protein MFA4 from porphyromonas gingivalis
Analyse Crystal structure of the fimbrial protein MFA4 from porphyromonas gingivalis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DHM
- Type
- protein
- Length
- 583 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Immunoreactive 32 kda antigen
- UniProt
- B2RHG4
- Pockets
- 3 · best druggability 0.32
Structure
x-ray diffraction · 4 distinct chains · 10% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Immunoreactive 32 kda antigen | protein | 28 | 0% helix, 61% strand | B2RHG4 |
| C | Immunoreactive 32 kda antigen | protein | 268 | 12% helix, 46% strand | B2RHG4 |
| B | Immunoreactive 32 kda antigen | protein | 21 | 0% helix, 81% strand | B2RHG4 |
| D | Immunoreactive 32 kda antigen | protein | 266 | 11% helix, 46% strand | B2RHG4 |
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 55 | 0.32 | 0.76 | 11 | empty |
| 2 | 52 | 0.29 | 0.75 | 16 | empty |
| 3 | 50 | 0.27 | 0.75 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1968 Ų buried · 55 hydrogen bonds · protein-protein
- B–D · 1853 Ų buried · 36 hydrogen bonds · protein-protein
- C–D · 59 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 9 modified (engineered).
Compared structures
- 5DHM · Crystal structure of the fimbrial protein Mfa4 from Porphyromonas gingivalis · the same entry in another collection · chain D against D, TM-score 1.00
- B2RHG4 · AlphaFold monomer V2.0 prediction for minor fimbrium tip subunit MFA4 (B2RHG4) · a predicted model of the same protein · chain D against A, TM-score 0.99
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 B2RHG4
- Elsewhere: RCSB PDB 5DHM · PDBe 5DHM · UniProt B2RHG4
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