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Crystal structure of precorrin-6Y C5,15-methyltransferase from geobacter metallireducens gs-15
Analyse Crystal structure of precorrin-6Y C5,15-methyltransferase from geobacter… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3E05
- Type
- protein
- Length
- 1,520 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Precorrin-6Y C5,15-methyltransferase (decarboxylating)
- EC
- 2.1.1.132
- UniProt
- Q39YF0
- Ligands
- CL
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 8 distinct chains · 32% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Precorrin-6Y C5,15-methyltransferase (decarboxylating) (EC 2.1.1.132) | protein | 188 | 32% helix, 26% strand | Q39YF0 |
| B | Precorrin-6Y C5,15-methyltransferase (decarboxylating) (EC 2.1.1.132) | protein | 192 | 31% helix, 25% strand | Q39YF0 |
| C | Precorrin-6Y C5,15-methyltransferase (decarboxylating) (EC 2.1.1.132) | protein | 190 | 33% helix, 25% strand | Q39YF0 |
| D | Precorrin-6Y C5,15-methyltransferase (decarboxylating) (EC 2.1.1.132) | protein | 192 | 31% helix, 26% strand | Q39YF0 |
| E | Precorrin-6Y C5,15-methyltransferase (decarboxylating) (EC 2.1.1.132) | protein | 191 | 31% helix, 25% strand | Q39YF0 |
| F | Precorrin-6Y C5,15-methyltransferase (decarboxylating) (EC 2.1.1.132) | protein | 187 | 32% helix, 26% strand | Q39YF0 |
| G | Precorrin-6Y C5,15-methyltransferase (decarboxylating) (EC 2.1.1.132) | protein | 189 | 32% helix, 25% strand | Q39YF0 |
| H | Precorrin-6Y C5,15-methyltransferase (decarboxylating) (EC 2.1.1.132) | protein | 191 | 31% helix, 25% strand | Q39YF0 |
Ligands and binding sites
- CL · Chloride ion · ion · 8 copies · chains A, B, C, D, E, F, G, H
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 978 | 0.85 | 0.86 | 113 | CL |
| 2 | 1184 | 0.83 | 0.84 | 120 | CL, GOL |
| 3 | 404 | 0.68 | 0.80 | 49 | empty |
| 4 | 409 | 0.66 | 0.79 | 47 | CL |
| 5 | 352 | 0.66 | 0.80 | 46 | CL |
Interfaces
15 interfaces between chains.
- E–G · 1532 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 1513 Ų buried · 21 hydrogen bonds · protein-protein
- F–H · 1478 Ų buried · 24 hydrogen bonds · protein-protein
- A–D · 1441 Ų buried · 23 hydrogen bonds · protein-protein
- D–E · 860 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 3E05 · CRYSTAL STRUCTURE OF Precorrin-6y C5,15-methyltransferase FROM Geobacter metallireducens… · 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 Q39YF0
- Elsewhere: RCSB PDB 3E05 · PDBe 3E05 · UniProt Q39YF0
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