MolNFT v1 · #72297 · protein
Crystal structure of mandelate RACEMASE/MUCONATE lactonizing protein from geobacillus sp. Y412MC10
3N4F: “Crystal structure of mandelate RACEMASE/MUCONATE lactonizing protein from geobacillus sp. Y412MC10”. X-ray diffraction, 1 ligand (MG), 14 pockets (best druggability 0.75). MolNFT v1 #72297 on GenesisL1: 3D structure, binding sites…
- PDB
- 3N4F
- Type
- protein
- Length
- 1,538 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mandelate RACEMASE/MUCONATE lactonizing protein
- UniProt
- D3EID5
- Ligands
- MG
- Pockets
- 14 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mandelate RACEMASE/MUCONATE lactonizing protein | protein | 390 | 35% helix, 26% strand | D3EID5 |
| B, C | Mandelate RACEMASE/MUCONATE lactonizing protein | protein | 386 | 35% helix, 26% strand | D3EID5 |
| D | Mandelate RACEMASE/MUCONATE lactonizing protein | protein | 376 | 34% helix, 26% strand | D3EID5 |
Ligands and binding sites
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 455 | 0.75 | 0.84 | 50 | empty |
| 2 | 302 | 0.73 | 0.86 | 48 | empty |
| 3 | 222 | 0.70 | 0.87 | 44 | empty |
| 4 | 158 | 0.64 | 0.86 | 32 | empty |
| 5 | 156 | 0.54 | 0.80 | 26 | empty |
Interfaces
5 interfaces between chains.
- A–B · 365 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 324 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 264 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 258 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 213 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 modified (engineered).
Compared structures
- 3N4F · CRYSTAL STRUCTURE OF Mandelate racemase/muconate lactonizing protein from Geobacillus sp.… · the same entry in another collection · chain A against A, 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 D3EID5
- Elsewhere: RCSB PDB 3N4F · PDBe 3N4F · UniProt D3EID5
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