Research workbench
Crystal structure of putative precorrin-6Y C5,15- methyltransferase targeted domain from corynebacterium diphtheriae
Analyse Crystal structure of putative precorrin-6Y C5,15- methyltransferase targeted… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HM2
- Type
- protein
- Length
- 1,353 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Precorrin-6Y C5,15-methyltransferase
- UniProt
- Q6NHA4
- Ligands
- MG, CA
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 8 distinct chains · 36% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Precorrin-6Y C5,15-methyltransferase | protein | 171 | 34% helix, 29% strand | Q6NHA4 |
| B | Precorrin-6Y C5,15-methyltransferase | protein | 171 | 33% helix, 29% strand | Q6NHA4 |
| C | Precorrin-6Y C5,15-methyltransferase | protein | 169 | 33% helix, 27% strand | Q6NHA4 |
| D | Precorrin-6Y C5,15-methyltransferase | protein | 167 | 39% helix, 28% strand | Q6NHA4 |
| E | Precorrin-6Y C5,15-methyltransferase | protein | 170 | 36% helix, 27% strand | Q6NHA4 |
| F | Precorrin-6Y C5,15-methyltransferase | protein | 167 | 35% helix, 29% strand | Q6NHA4 |
| G | Precorrin-6Y C5,15-methyltransferase | protein | 171 | 37% helix, 30% strand | Q6NHA4 |
| H | Precorrin-6Y C5,15-methyltransferase | protein | 167 | 39% helix, 26% strand | Q6NHA4 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains B, G
- CA · Calcium ion · metal · 2 copies · chains D, F, B, G
- ACY · Acetic acid · additive · 3 copies · chains A, D, 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, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 632 | 0.88 | 0.92 | 78 | empty |
| 2 | 604 | 0.86 | 0.92 | 77 | empty |
| 3 | 1019 | 0.76 | 0.78 | 79 | empty |
| 4 | 764 | 0.71 | 0.77 | 73 | empty |
| 5 | 327 | 0.65 | 0.81 | 26 | empty |
Interfaces
16 interfaces between chains.
- A–C · 983 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 971 Ų buried · 19 hydrogen bonds · protein-protein
- F–H · 941 Ų buried · 14 hydrogen bonds · protein-protein
- E–G · 936 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 630 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 3HM2 · Crystal Structure of Putative Precorrin-6Y C5,15-Methyltransferase Targeted Domain from… · 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 Q6NHA4
- Elsewhere: RCSB PDB 3HM2 · PDBe 3HM2 · UniProt Q6NHA4
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