Research workbench
Crystal structure of human ZCCHC4 in complex with sah
Analyse Crystal structure of human ZCCHC4 in complex with sah in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6UCA
- Type
- protein
- Length
- 2,409 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RRNA N6-adenosine-methyltransferase ZCCHC4
- EC
- 2.1.1.-
- UniProt
- Q9H5U6
- Ligands
- SAH, ZN
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 6 distinct chains · 29% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RRNA N6-adenosine-methyltransferase ZCCHC4 (EC 2.1.1.-) | protein | 413 | 29% helix, 20% strand | Q9H5U6 |
| B | RRNA N6-adenosine-methyltransferase ZCCHC4 (EC 2.1.1.-) | protein | 393 | 29% helix, 19% strand | Q9H5U6 |
| C | RRNA N6-adenosine-methyltransferase ZCCHC4 (EC 2.1.1.-) | protein | 387 | 30% helix, 19% strand | Q9H5U6 |
| D | RRNA N6-adenosine-methyltransferase ZCCHC4 (EC 2.1.1.-) | protein | 416 | 29% helix, 21% strand | Q9H5U6 |
| E | RRNA N6-adenosine-methyltransferase ZCCHC4 (EC 2.1.1.-) | protein | 402 | 29% helix, 19% strand | Q9H5U6 |
| F | RRNA N6-adenosine-methyltransferase ZCCHC4 (EC 2.1.1.-) | protein | 398 | 27% helix, 18% strand | Q9H5U6 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 6 copies · chains A, B, C, D, E, F
- ZN · Zinc ion · metal · 36 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1076 | 0.78 | 0.80 | 103 | empty |
| 2 | 109 | 0.78 | 0.97 | 29 | SAH |
| 3 | 111 | 0.77 | 0.96 | 32 | SAH |
| 4 | 776 | 0.77 | 0.81 | 92 | empty |
| 5 | 133 | 0.76 | 0.94 | 29 | SAH |
Interfaces
9 interfaces between chains.
- A–D · 1157 Ų buried · 9 hydrogen bonds · protein-protein
- D–E · 600 Ų buried · 2 hydrogen bonds · protein-protein
- C–E · 548 Ų buried · 9 hydrogen bonds · protein-protein
- B–F · 530 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 402 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6UCA · Crystal structure of human ZCCHC4 in complex with SAH · the same entry in another collection · chain F against F, TM-score 1.00
- Q9H5U6 · AlphaFold monomer V2.0 prediction for rRNA N6-adenosine- methyltransferase ZCCHC4 (Q9H5U6) · a predicted model of the same protein · chain E 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 Q9H5U6
- Elsewhere: RCSB PDB 6UCA · PDBe 6UCA · UniProt Q9H5U6
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