MolNFT v1 · #93812 · protein
Crystal structure of arsab in complex with 5,6-dimethylbenzimidazole
4HDR: “Crystal structure of arsab in complex with 5,6-dimethylbenzimidazole”. X-ray diffraction, 1 ligand (DMD), 9 pockets (best druggability 0.70). MolNFT v1 #93812 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4HDR
- Type
- protein
- Length
- 1,323 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Arsa; Arsb
- EC
- 2.4.2.21
- UniProt
- F6MZ55, F6MZ56
- Ligands
- DMD
- Pockets
- 9 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 52% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Arsa (EC 2.4.2.21) | protein | 335 | 52% helix, 11% strand | F6MZ55 |
| B | Arsb (EC 2.4.2.21) | protein | 329 | 52% helix, 11% strand | F6MZ56 |
| C | Arsa (EC 2.4.2.21) | protein | 331 | 52% helix, 11% strand | F6MZ55 |
| D | Arsb (EC 2.4.2.21) | protein | 328 | 52% helix, 11% strand | F6MZ56 |
Ligands and binding sites
- DMD · 5,6-dimethylbenzimidazole · ligand · 2 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 13 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 706 | 0.70 | 0.77 | 64 | empty |
| 2 | 461 | 0.67 | 0.79 | 59 | DMD, EDO |
| 3 | 348 | 0.67 | 0.81 | 47 | empty |
| 4 | 347 | 0.66 | 0.81 | 56 | empty |
| 5 | 363 | 0.65 | 0.79 | 38 | DMD, EDO |
Interfaces
3 interfaces between chains.
- A–B · 1817 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1781 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 103 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4HDR · Crystal Structure of ArsAB in Complex with 5,6-dimethylbenzimidazole · 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 F6MZ55
- Every structure of UniProt F6MZ56
- Elsewhere: RCSB PDB 4HDR · PDBe 4HDR · UniProt F6MZ55 · UniProt F6MZ56
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