Research workbench
Crystal structure of S-adenosylmethionine synthetase from burkholderia pseudomallei
Analyse Crystal structure of S-adenosylmethionine synthetase from burkholderia… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IML
- Type
- protein
- Length
- 1,379 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S-adenosylmethionine synthetase
- EC
- 2.5.1.6
- UniProt
- Q63YH5
- Pockets
- 14 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | S-adenosylmethionine synthetase (EC 2.5.1.6) | protein | 368 | 33% helix, 25% strand | Q63YH5 |
| B | S-adenosylmethionine synthetase (EC 2.5.1.6) | protein | 357 | 34% helix, 24% strand | Q63YH5 |
| C | S-adenosylmethionine synthetase (EC 2.5.1.6) | protein | 343 | 33% helix, 27% strand | Q63YH5 |
| D | S-adenosylmethionine synthetase (EC 2.5.1.6) | protein | 311 | 31% helix, 25% strand | Q63YH5 |
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 634 | 0.75 | 0.81 | 67 | empty |
| 2 | 523 | 0.72 | 0.81 | 64 | empty |
| 3 | 483 | 0.70 | 0.80 | 50 | empty |
| 4 | 437 | 0.69 | 0.81 | 47 | empty |
| 5 | 467 | 0.66 | 0.79 | 50 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2321 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 2077 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 523 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 405 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 82 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3IML · Crystal Structure Of S-Adenosylmethionine Synthetase From Burkholderia Pseudomallei · the same entry in another collection · chain D against D, TM-score 1.00
- Q63YH5 · AlphaFold monomer V2.0 prediction for S-adenosylmethionine synthase (Q63YH5) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q63YH5
- Elsewhere: RCSB PDB 3IML · PDBe 3IML · UniProt Q63YH5
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