MolNFT v1 · #122186 · protein
Crystal structure of cobyrinic acid A,C-diamide synthase from mycobacterium smegmatis with bound ADP and magnesium
5IHP: “Crystal structure of cobyrinic acid A,C-diamide synthase from mycobacterium smegmatis with bound ADP and…”. X-ray diffraction, 2 ligands (ADP, MG), 3 pockets (best druggability 0.48). MolNFT v1 #122186 on GenesisL1: 3D structure…
- PDB
- 5IHP
- Type
- protein
- Length
- 491 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cobyrinic acid A,C-diamide synthase
- UniProt
- A0QTQ5
- Ligands
- ADP, MG
- Pockets
- 3 · best druggability 0.48
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cobyrinic acid A,C-diamide synthase | protein | 246 | 43% helix, 16% strand | A0QTQ5 |
| B | Cobyrinic acid A,C-diamide synthase | protein | 245 | 43% helix, 16% strand | A0QTQ5 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 67 | 0.48 | 0.85 | 18 | empty |
| 2 | 63 | 0.38 | 0.79 | 18 | empty |
| 3 | 60 | 0.35 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 218 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5IHP · Crystal Structure of Cobyrinic Acid a,c-diamide synthase from Mycobacterium smegmatis… · 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 A0QTQ5
- Elsewhere: RCSB PDB 5IHP · PDBe 5IHP · UniProt A0QTQ5
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