Research workbench
Crystal structure of putative mandelate RACEMASE/MUCONATELACTONIZING enzyme from roseovarius nubinhibens ism complexed with magnesium
Analyse Crystal structure of putative mandelate RACEMASE/MUCONATELACTONIZING enzyme… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FV9
- Type
- protein
- Length
- 2,968 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mandelate RACEMASE/MUCONATE lactonizing enzyme
- UniProt
- A3SNG0
- Ligands
- MG
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G, D, E, F | Mandelate RACEMASE/MUCONATE lactonizing enzyme | protein | 373 | 37% helix, 23% strand | A3SNG0 |
| A | Mandelate RACEMASE/MUCONATE lactonizing enzyme | protein | 363 | 38% helix, 22% strand | A3SNG0 |
| B | Mandelate RACEMASE/MUCONATE lactonizing enzyme | protein | 365 | 38% helix, 22% strand | A3SNG0 |
| H, C | Mandelate RACEMASE/MUCONATE lactonizing enzyme | protein | 374 | 36% helix, 23% strand | A3SNG0 |
Ligands and binding sites
- MG · Magnesium ion · metal · 5 copies · chains A, E, F, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1032 | 0.88 | 0.90 | 145 | empty |
| 2 | 588 | 0.85 | 0.91 | 85 | empty |
| 3 | 493 | 0.82 | 0.89 | 75 | empty |
| 4 | 323 | 0.82 | 0.92 | 65 | empty |
| 5 | 223 | 0.80 | 0.93 | 36 | empty |
Interfaces
16 interfaces between chains.
- F–B · 1169 Ų buried · 10 hydrogen bonds · protein-protein
- G–E · 1162 Ų buried · 11 hydrogen bonds · protein-protein
- A–H · 1155 Ų buried · 12 hydrogen bonds · protein-protein
- D–C · 1132 Ų buried · 12 hydrogen bonds · protein-protein
- E–C · 1053 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 3FV9 · Crystal structure of putative mandelate racemase/muconatelactonizing enzyme from… · the same entry in another collection · chain E against E, 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 A3SNG0
- Elsewhere: RCSB PDB 3FV9 · PDBe 3FV9 · UniProt A3SNG0
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