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Crystal structure of cdi complex from cupriavidus taiwanensis lmg 19424
Analyse Crystal structure of cdi complex from cupriavidus taiwanensis lmg 19424 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5T87
- Type
- protein
- Length
- 745 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cdii immunity protein; Cdia toxin
- UniProt
- B3R1C2, B3R1C1
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 7 distinct chains · 49% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cdii immunity protein | protein | 114 | 72% helix, 2% strand | B3R1C2 |
| B | Cdii immunity protein | protein | 113 | 69% helix, 2% strand | B3R1C2 |
| C, D | Cdii immunity protein | protein | 115 | 68% helix, 2% strand | B3R1C2 |
| E | Cdia toxin | protein | 69 | 25% helix, 38% strand | B3R1C1 |
| F | Cdia toxin | protein | 74 | 24% helix, 32% strand | B3R1C1 |
| G | Cdia toxin | protein | 75 | 25% helix, 37% strand | B3R1C1 |
| H | Cdia toxin | protein | 70 | 26% helix, 30% strand | B3R1C1 |
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 717 | 0.73 | 0.79 | 71 | empty |
| 2 | 763 | 0.69 | 0.76 | 84 | empty |
| 3 | 61 | 0.38 | 0.80 | 20 | empty |
| 4 | 66 | 0.38 | 0.79 | 20 | empty |
| 5 | 51 | 0.37 | 0.81 | 19 | empty |
Interfaces
11 interfaces between chains.
- B–F · 1192 Ų buried · 20 hydrogen bonds · protein-protein
- C–G · 1169 Ų buried · 20 hydrogen bonds · protein-protein
- A–E · 1162 Ų buried · 21 hydrogen bonds · protein-protein
- D–H · 1149 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 461 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 5T87 · Crystal structure of CDI complex from Cupriavidus taiwanensis LMG 19424 · 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 B3R1C2
- Every structure of UniProt B3R1C1
- Elsewhere: RCSB PDB 5T87 · PDBe 5T87 · UniProt B3R1C2 · UniProt B3R1C1
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