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Crystal Structure Analysis of the S-adenosyl-L-methionine dependent uroporphyrinogen-III C-methyltransferase SUMT
Analyse Crystal Structure Analysis of the S-adenosyl-L-methionine dependent… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1S4D
- Type
- protein
- Length
- 3,075 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.7
- Source
- Pseudomonas denitrificans
- Molecule
- Uroporphyrin-III C-methyltransferase
- EC
- 2.1.1.107
- UniProt
- P21631
- Ligands
- SAH
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · resolution 2.7 · 12 distinct chains · 31% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uroporphyrin-III C-methyltransferase (EC 2.1.1.107) | protein | 256 | 31% helix, 20% strand | P21631 |
| B | Uroporphyrin-III C-methyltransferase (EC 2.1.1.107) | protein | 263 | 32% helix, 22% strand | P21631 |
| D | Uroporphyrin-III C-methyltransferase (EC 2.1.1.107) | protein | 248 | 32% helix, 22% strand | P21631 |
| E | Uroporphyrin-III C-methyltransferase (EC 2.1.1.107) | protein | 265 | 33% helix, 20% strand | P21631 |
| F | Uroporphyrin-III C-methyltransferase (EC 2.1.1.107) | protein | 254 | 27% helix, 21% strand | P21631 |
| G | Uroporphyrin-III C-methyltransferase (EC 2.1.1.107) | protein | 258 | 31% helix, 22% strand | P21631 |
| H | Uroporphyrin-III C-methyltransferase (EC 2.1.1.107) | protein | 259 | 31% helix, 20% strand | P21631 |
| I | Uroporphyrin-III C-methyltransferase (EC 2.1.1.107) | protein | 263 | 32% helix, 20% strand | P21631 |
| J | Uroporphyrin-III C-methyltransferase (EC 2.1.1.107) | protein | 252 | 30% helix, 20% strand | P21631 |
| K | Uroporphyrin-III C-methyltransferase (EC 2.1.1.107) | protein | 258 | 31% helix, 22% strand | P21631 |
| L | Uroporphyrin-III C-methyltransferase (EC 2.1.1.107) | protein | 247 | 31% helix, 21% strand | P21631 |
| M | Uroporphyrin-III C-methyltransferase (EC 2.1.1.107) | protein | 252 | 30% helix, 20% strand | P21631 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 12 copies · chains A, B, D, E, F, G, H, I, J, K, L, M
- GOL · Glycerol · additive · 26 copies · chains A, B, D, E, F, G, H, I, J, K, L, M
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 | 778 | 0.74 | 0.79 | 67 | empty |
| 2 | 587 | 0.73 | 0.81 | 64 | GOL, SAH |
| 3 | 606 | 0.73 | 0.81 | 59 | GOL, SAH |
| 4 | 625 | 0.73 | 0.80 | 58 | GOL, SAH |
| 5 | 532 | 0.73 | 0.81 | 67 | empty |
Interfaces
13 interfaces between chains.
- J–K · 2686 Ų buried · 27 hydrogen bonds · protein-protein
- D–E · 2665 Ų buried · 28 hydrogen bonds · protein-protein
- H–I · 2645 Ų buried · 25 hydrogen bonds · protein-protein
- F–G · 2639 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 2592 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 1S4D · Crystal structure analysis of the S-adenosyl-L-methionine dependent uroporphyrinogen-III… · the same entry in another collection · chain M against M, 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 P21631
- Elsewhere: RCSB PDB 1S4D · PDBe 1S4D · UniProt P21631
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