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Crystal structure of paracoccus denitrificans aztd
Analyse Crystal structure of paracoccus denitrificans aztd in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CK1
- Type
- protein
- Length
- 1,488 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- A1B2F4 protein
- UniProt
- A1B2F4
- Ligands
- ZN
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 3% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | A1B2F4 protein | protein | 372 | 2% helix, 52% strand | A1B2F4 |
| A | A1B2F4 protein | protein | 375 | 3% helix, 55% strand | A1B2F4 |
| C | A1B2F4 protein | protein | 366 | 3% helix, 54% strand | A1B2F4 |
| D | A1B2F4 protein | protein | 375 | 2% helix, 55% strand | A1B2F4 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains B, A, C, D
- PEG · Di(hydroxyethyl)ether · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1017 | 0.78 | 0.80 | 63 | ZN |
| 2 | 1013 | 0.78 | 0.80 | 68 | ZN |
| 3 | 1185 | 0.78 | 0.80 | 81 | empty |
| 4 | 1193 | 0.77 | 0.79 | 71 | empty |
| 5 | 112 | 0.40 | 0.76 | 22 | empty |
Interfaces
5 interfaces between chains.
- A–C · 641 Ų buried · 6 hydrogen bonds · protein-protein
- B–A · 589 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 182 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 117 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 13 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6CK1 · Crystal structure of Paracoccus denitrificans AztD · the same entry in another collection · chain B against B, 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 A1B2F4
- Elsewhere: RCSB PDB 6CK1 · PDBe 6CK1 · UniProt A1B2F4
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