Research workbench
Catabolic reductive dehalogenase nprdha, N-terminally tagged, K488Q variant
Analyse Catabolic reductive dehalogenase nprdha, N-terminally tagged, K488Q variant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZY0
- Type
- protein
- Length
- 2,092 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oxidoreductase, NAD-BINDING/IRON-sulfur cluster-binding protein
- UniProt
- K2MB66
- Ligands
- SF4, B12, NA, CL
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Oxidoreductase, NAD-BINDING/IRON-sulfur cluster-binding protein | protein | 701 | 37% helix, 13% strand | K2MB66 |
| B | Oxidoreductase, NAD-BINDING/IRON-sulfur cluster-binding protein | protein | 695 | 36% helix, 13% strand | K2MB66 |
| C | Oxidoreductase, NAD-BINDING/IRON-sulfur cluster-binding protein | protein | 696 | 36% helix, 13% strand | K2MB66 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 6 copies · chains A, B, C
- B12 · Cobalamin · ligand · 3 copies · chains A, B, C
- NA · Sodium ion · metal · 3 copies · chains A, B, C
- CL · Chloride ion · ion · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1075 | 0.87 | 0.87 | 90 | SF4, B12, CL |
| 2 | 1102 | 0.87 | 0.87 | 93 | SF4, B12, CL |
| 3 | 1094 | 0.86 | 0.87 | 93 | SF4, B12 |
| 4 | 1009 | 0.86 | 0.87 | 81 | empty |
| 5 | 1035 | 0.86 | 0.87 | 79 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1234 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 167 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 26 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6ZY0 · Catabolic reductive dehalogenase NpRdhA, N-terminally tagged, K488Q variant · 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 K2MB66
- Elsewhere: RCSB PDB 6ZY0 · PDBe 6ZY0 · UniProt K2MB66
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