MolNFT v1 · #157353 · protein
Crystal structure of ATPase module of SMCHD1 bound to ATP
6MW7 · Structural maintenance of chromosomes flexible hinge…: “Crystal structure of ATPase module of SMCHD1 bound to ATP”. X-ray diffraction, 4 ligands (ATP, MG, NA), 20 pockets (best druggability 0.81). MolNFT v1 #157353 on GenesisL1: 3D…
- PDB
- 6MW7
- Type
- protein
- Length
- 2,040 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Structural maintenance of chromosomes flexible hinge domain-containing protein 1
- EC
- 3.6.1.-
- UniProt
- A6NHR9
- Ligands
- ATP, MG, NA, SO4
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 28% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Structural maintenance of chromosomes flexible hinge domain-containing protein 1 (EC 3.6.1.-) | protein | 514 | 28% helix, 27% strand | A6NHR9 |
| B | Structural maintenance of chromosomes flexible hinge domain-containing protein 1 (EC 3.6.1.-) | protein | 502 | 29% helix, 27% strand | A6NHR9 |
| C | Structural maintenance of chromosomes flexible hinge domain-containing protein 1 (EC 3.6.1.-) | protein | 519 | 27% helix, 27% strand | A6NHR9 |
| D | Structural maintenance of chromosomes flexible hinge domain-containing protein 1 (EC 3.6.1.-) | protein | 505 | 29% helix, 27% strand | A6NHR9 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · chains C
- SO4 · Sulfate ion · ion · chains 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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 347 | 0.81 | 0.91 | 50 | ATP, SO4, MG, NA |
| 2 | 440 | 0.79 | 0.87 | 49 | ATP, MG |
| 3 | 377 | 0.76 | 0.87 | 46 | ATP, MG |
| 4 | 515 | 0.76 | 0.84 | 66 | empty |
| 5 | 1068 | 0.76 | 0.78 | 93 | empty |
Interfaces
4 interfaces between chains.
- C–D · 3070 Ų buried · 47 hydrogen bonds · protein-protein
- A–B · 3013 Ų buried · 47 hydrogen bonds · protein-protein
- B–C · 144 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 96 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 modified (engineered).
Compared structures
- 6MW7 · Crystal structure of ATPase module of SMCHD1 bound to ATP · the same entry in another collection · chain D against D, TM-score 1.00
- A6NHR9 · AlphaFold monomer V2.0 prediction for structural maintenance of chromosomes flexible… · a predicted model of the same protein · chain D against A, TM-score 0.98
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 A6NHR9
- Elsewhere: RCSB PDB 6MW7 · PDBe 6MW7 · UniProt A6NHR9
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