Research workbench
X-ray structure of the KIJD1 C3-methyltransfeerase, converted to monomeric form
Analyse X-ray structure of the KIJD1 C3-methyltransfeerase, converted to monomeric form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5T6B
- Type
- protein
- Length
- 1,596 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sugar 3-C-methyl transferase
- UniProt
- B3TMQ9
- Ligands
- SAH, TMP, ZN
- Pockets
- 16 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sugar 3-C-methyl transferase | protein | 403 | 37% helix, 24% strand | B3TMQ9 |
| B | Sugar 3-C-methyl transferase | protein | 406 | 39% helix, 24% strand | B3TMQ9 |
| C | Sugar 3-C-methyl transferase | protein | 394 | 40% helix, 24% strand | B3TMQ9 |
| D | Sugar 3-C-methyl transferase | protein | 393 | 40% helix, 24% strand | B3TMQ9 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 4 copies · chains A, B, C, D
- TMP · Thymidine-5'-phosphate · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 602 | 0.82 | 0.87 | 76 | SAH, TMP |
| 2 | 1060 | 0.81 | 0.82 | 96 | SAH, TMP |
| 3 | 1137 | 0.78 | 0.80 | 112 | MES |
| 4 | 765 | 0.75 | 0.80 | 65 | SAH, TMP |
| 5 | 778 | 0.72 | 0.78 | 67 | SAH, TMP |
Interfaces
6 interfaces between chains.
- B–D · 962 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 754 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 207 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 192 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 133 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5T6B · X-ray structure of the KijD1 C3-methyltransfeerase, converted to monomeric form · the same entry in another collection · chain D against D, 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 B3TMQ9
- Elsewhere: RCSB PDB 5T6B · PDBe 5T6B · UniProt B3TMQ9
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