Research workbench
Structural insights of mat enzymes: MATA2B complexed with adenosine and pyrophosphate
Analyse Structural insights of mat enzymes: MATA2B complexed with adenosine and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KTV
- Type
- protein
- Length
- 2,089 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S-adenosylmethionine synthase isoform type-2; Methionine adenosyltransferase 2 subunit…
- EC
- 2.5.1.6
- UniProt
- P31153, Q9NZL9
- Ligands
- ADN, POP, MG, PO4
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 34% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | S-adenosylmethionine synthase isoform type-2 (EC 2.5.1.6) | protein | 362 | 31% helix, 26% strand | P31153 |
| B, D | S-adenosylmethionine synthase isoform type-2 (EC 2.5.1.6) | protein | 381 | 30% helix, 26% strand | P31153 |
| C | S-adenosylmethionine synthase isoform type-2 (EC 2.5.1.6) | protein | 361 | 33% helix, 28% strand | P31153 |
| E | Methionine adenosyltransferase 2 subunit beta | protein | 309 | 40% helix, 15% strand | Q9NZL9 |
| F | Methionine adenosyltransferase 2 subunit beta | protein | 295 | 36% helix, 12% strand | Q9NZL9 |
Ligands and binding sites
- ADN · Adenosine · ligand · 2 copies · chains A, B, C, D
- POP · Pyrophosphate 2- · ligand · chains C, D
- MG · Magnesium ion · metal · chains C, D
- PO4 · Phosphate ion · ion · chains A, B
- EDO · 1,2-ethanediol · additive · 12 copies · chains A, B, F, D, C, E
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 | 250 | 0.83 | 0.95 | 41 | ADN, POP, EDO, MG |
| 2 | 261 | 0.83 | 0.95 | 41 | ADN, PO4, EDO |
| 3 | 1157 | 0.79 | 0.80 | 104 | EDO |
| 4 | 815 | 0.74 | 0.79 | 77 | EDO |
| 5 | 613 | 0.69 | 0.78 | 61 | empty |
Interfaces
10 interfaces between chains.
- C–D · 2496 Ų buried · 42 hydrogen bonds · protein-protein
- A–B · 2376 Ų buried · 35 hydrogen bonds · protein-protein
- D–E · 1019 Ų buried · 12 hydrogen bonds · protein-protein
- B–F · 1003 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 567 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4KTV · Structural insights of MAT enzymes: MATa2b complexed with adenosine and pyrophosphate · the same entry in another collection · chain F against F, TM-score 1.00
- P31153 · AlphaFold monomer V2.0 prediction for S-adenosylmethionine synthase isoform type-2… · a predicted model of the same protein · chain B against A, TM-score 0.99
- Q9NZL9 · AlphaFold monomer V2.0 prediction for methionine adenosyltransferase 2 subunit beta… · a predicted model of the same protein · chain E against A, TM-score 0.96
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 P31153
- Every structure of UniProt Q9NZL9
- Elsewhere: RCSB PDB 4KTV · PDBe 4KTV · UniProt P31153 · UniProt Q9NZL9
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