Research workbench
Mdba protein, a thiol-disulfide oxidoreductase from corynebacterium diphtheriae
Analyse Mdba protein, a thiol-disulfide oxidoreductase from corynebacterium diphtheriae in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5C00
- Type
- protein
- Length
- 792 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mdba protein
- UniProt
- Q6NFK7
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Mdba protein | protein | 202 | 50% helix, 16% strand | Q6NFK7 |
| C | Mdba protein | protein | 197 | 50% helix, 16% strand | Q6NFK7 |
| D | Mdba protein | protein | 191 | 48% helix, 17% strand | Q6NFK7 |
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 473 | 0.76 | 0.84 | 52 | empty |
| 2 | 856 | 0.75 | 0.79 | 96 | empty |
| 3 | 319 | 0.71 | 0.84 | 41 | empty |
| 4 | 108 | 0.38 | 0.75 | 18 | empty |
| 5 | 52 | 0.32 | 0.78 | 13 | empty |
Interfaces
5 interfaces between chains.
- A–B · 959 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 703 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 532 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 238 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 226 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 5C00 · MdbA protein, a thiol-disulfide oxidoreductase from Corynebacterium diphtheriae · 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 Q6NFK7
- Elsewhere: RCSB PDB 5C00 · PDBe 5C00 · UniProt Q6NFK7
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