Research workbench
Crystal structure of chlorite dismutase from D. aromatica at pH 9.0
Analyse Crystal structure of chlorite dismutase from D. aromatica at pH 9.0 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3Q09
- Type
- protein
- Length
- 4,820 residues
- Chains
- 20
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chlorite dismutase
- EC
- 1.13.11.49
- UniProt
- Q47CX0
- Ligands
- HEM, CA, NO2
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T | Chlorite dismutase (EC 1.13.11.49) | protein | 241 | 39% helix, 28% strand | Q47CX0 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 20 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T
- CA · Calcium ion · metal · 20 copies · chains A, D, B, C, E, F, G, H, I, J, K, L, M, N, O, P, T, Q, R, S
- NO2 · Nitrite ion · ion · 20 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 975 | 0.85 | 0.86 | 90 | HEM, NO2 |
| 2 | 1119 | 0.84 | 0.85 | 111 | HEM, NO2 |
| 3 | 930 | 0.83 | 0.84 | 91 | HEM, NO2 |
| 4 | 624 | 0.82 | 0.87 | 85 | HEM, NO2 |
| 5 | 637 | 0.81 | 0.85 | 63 | HEM, NO2 |
Interfaces
36 interfaces between chains.
- Q–R · 1611 Ų buried · 31 hydrogen bonds · protein-protein
- R–S · 1596 Ų buried · 25 hydrogen bonds · protein-protein
- P–S · 1594 Ų buried · 24 hydrogen bonds · protein-protein
- Q–T · 1591 Ų buried · 25 hydrogen bonds · protein-protein
- N–O · 1590 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 3Q09 · Crystal Structure of Chlorite Dismutase from D. Aromatica at pH 9.0 · the same entry in another collection · chain E against E, 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 Q47CX0
- Elsewhere: RCSB PDB 3Q09 · PDBe 3Q09 · UniProt Q47CX0
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