Research workbench
Crystal structure of MNMC2 from aquifex aeolicus
Analyse Crystal structure of MNMC2 from aquifex aeolicus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VYW
- Type
- protein
- Length
- 1,219 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MNMC2
- UniProt
- O67789
- Ligands
- SAM, BEN
- Pockets
- 15 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MNMC2 | protein | 303 | 40% helix, 21% strand | O67789 |
| B, C | MNMC2 | protein | 305 | 39% helix, 21% strand | O67789 |
| D | MNMC2 | protein | 306 | 39% helix, 20% strand | O67789 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 4 copies · chains A, B, C, D
- BEN · Benzamidine · ligand · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1003 | 0.80 | 0.81 | 98 | SAM |
| 2 | 1125 | 0.77 | 0.79 | 86 | empty |
| 3 | 125 | 0.74 | 0.94 | 28 | SAM |
| 4 | 129 | 0.73 | 0.93 | 29 | SAM |
| 5 | 310 | 0.70 | 0.84 | 49 | SAM |
Interfaces
4 interfaces between chains.
- B–D · 580 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 545 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 470 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 48 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 3VYW · Crystal structure of MNMC2 from Aquifex Aeolicus · the same entry in another collection · chain B against B, 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 O67789
- Elsewhere: RCSB PDB 3VYW · PDBe 3VYW · UniProt O67789
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