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Crystal structure of an enolase (mandelate racemase subgroup) from labrenzia aggregata iam 12614 (target nysgrc-012903) with bound mg, space group P212121
Analyse Crystal structure of an enolase (mandelate racemase subgroup) from labrenzia… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MGG
- Type
- protein
- Length
- 2,894 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Muconate lactonizing enzyme
- UniProt
- A0NXQ8
- Ligands
- MG, NI, CL
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 6 distinct chains · 39% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Muconate lactonizing enzyme | protein | 369 | 38% helix, 23% strand | A0NXQ8 |
| B | Muconate lactonizing enzyme | protein | 361 | 39% helix, 23% strand | A0NXQ8 |
| C | Muconate lactonizing enzyme | protein | 367 | 37% helix, 23% strand | A0NXQ8 |
| D, E | Muconate lactonizing enzyme | protein | 361 | 39% helix, 23% strand | A0NXQ8 |
| F, H | Muconate lactonizing enzyme | protein | 362 | 39% helix, 23% strand | A0NXQ8 |
| G | Muconate lactonizing enzyme | protein | 351 | 40% helix, 22% strand | A0NXQ8 |
Ligands and binding sites
- MG · Magnesium ion · metal · 17 copies · chains A, E, B, D, C, G, H, F
- NI · Nickel (II) ion · metal · 3 copies · chains A, G, C, E, D, H
- CL · Chloride ion · ion · 3 copies · chains A, B, G
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 | 885 | 0.82 | 0.84 | 93 | empty |
| 2 | 755 | 0.81 | 0.85 | 88 | empty |
| 3 | 720 | 0.81 | 0.85 | 78 | empty |
| 4 | 652 | 0.80 | 0.85 | 76 | empty |
| 5 | 438 | 0.76 | 0.85 | 79 | empty |
Interfaces
16 interfaces between chains.
- C–H · 1031 Ų buried · 9 hydrogen bonds · protein-protein
- E–G · 1011 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1010 Ų buried · 9 hydrogen bonds · protein-protein
- D–F · 1004 Ų buried · 10 hydrogen bonds · protein-protein
- C–G · 673 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 4MGG · Crystal structure of an enolase (mandelate racemase subgroup) from labrenzia aggregata… · the same entry in another collection · chain H against H, TM-score 1.00
- A0NXQ8 · AlphaFold monomer V2.0 prediction for cis-3-hydroxy-L-proline dehydratase (A0NXQ8) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 A0NXQ8
- Elsewhere: RCSB PDB 4MGG · PDBe 4MGG · UniProt A0NXQ8
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