Research workbench
Structural insights of mat enzymes: MATA2B complexed with SAM and ppnp
Analyse Structural insights of mat enzymes: MATA2B complexed with SAM and ppnp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NDN
- Type
- protein
- Length
- 2,100 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
- PPK, SAM, MG
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 6 distinct chains · 35% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | S-adenosylmethionine synthase isoform type-2 (EC 2.5.1.6) | protein | 362 | 33% helix, 27% strand | P31153 |
| B | S-adenosylmethionine synthase isoform type-2 (EC 2.5.1.6) | protein | 383 | 32% helix, 26% strand | P31153 |
| C | S-adenosylmethionine synthase isoform type-2 (EC 2.5.1.6) | protein | 360 | 34% helix, 28% strand | P31153 |
| D | S-adenosylmethionine synthase isoform type-2 (EC 2.5.1.6) | protein | 382 | 33% helix, 26% strand | P31153 |
| E | Methionine adenosyltransferase 2 subunit beta | protein | 309 | 42% helix, 17% strand | Q9NZL9 |
| F | Methionine adenosyltransferase 2 subunit beta | protein | 304 | 39% helix, 17% strand | Q9NZL9 |
Ligands and binding sites
- PPK · (diphosphono)aminophosphonic acid · ligand · 2 copies · chains A, B, C, D
- SAM · S-adenosylmethionine · ligand · 2 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 17 copies · chains A, B, D, F, 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 275 | 0.82 | 0.94 | 46 | MG, PPK, SAM |
| 2 | 269 | 0.82 | 0.94 | 50 | MG, PPK, SAM |
| 3 | 989 | 0.79 | 0.80 | 95 | EDO |
| 4 | 644 | 0.72 | 0.79 | 64 | empty |
| 5 | 773 | 0.72 | 0.78 | 80 | EDO |
Interfaces
10 interfaces between chains.
- C–D · 2551 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 2497 Ų buried · 34 hydrogen bonds · protein-protein
- B–F · 1064 Ų buried · 12 hydrogen bonds · protein-protein
- D–E · 1034 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 553 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 4NDN · Structural insights of MAT enzymes: MATa2b complexed with SAM and PPNP · the same entry in another collection · chain E against E, 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 D 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 4NDN · PDBe 4NDN · UniProt P31153 · UniProt Q9NZL9
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