MolNFT v1 · #142708 · protein
Crystal structure of mycobacterium smegmatis mfd in complex with ADP + pi at 3.5 a resolution.
6ACX: “Crystal structure of mycobacterium smegmatis mfd in complex with ADP + pi at 3.5 a resolution.”. X-ray diffraction, 3 ligands (ADP, SO4, PO4), 20 pockets (best druggability 0.83). MolNFT v1 #142708 on GenesisL1: 3D structure…
- PDB
- 6ACX
- Type
- protein
- Length
- 2,343 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mycobacterium smegmatis mfd
- EC
- 3.6.4.-
- UniProt
- I7G7M2
- Ligands
- ADP, SO4, PO4
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mycobacterium smegmatis mfd (EC 3.6.4.-) | protein | 1175 | 39% helix, 18% strand | I7G7M2 |
| B | Mycobacterium smegmatis mfd (EC 3.6.4.-) | protein | 1168 | 40% helix, 17% strand | I7G7M2 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- PO4 · Phosphate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 956 | 0.83 | 0.85 | 111 | empty |
| 2 | 951 | 0.83 | 0.84 | 100 | ADP |
| 3 | 425 | 0.74 | 0.84 | 58 | empty |
| 4 | 973 | 0.73 | 0.77 | 76 | PO4, ADP |
| 5 | 112 | 0.73 | 0.94 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 981 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6ACX · Crystal structure of Mycobacterium smegmatis Mfd in complex with ADP + Pi at 3.5 A… · 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 I7G7M2
- Elsewhere: RCSB PDB 6ACX · PDBe 6ACX · UniProt I7G7M2
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