Research workbench
Crystal structure of an enolase (mandalate racemase subgroup, target efi-502101) from pelagibaca bermudensis HTCC2601, with bound mg and L-4-hydroxyproline betaine (betonicine)
Analyse Crystal structure of an enolase (mandalate racemase subgroup, target… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4H2H
- Type
- protein
- Length
- 2,925 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mandelate RACEMASE/MUCONATE lactonizing enzyme
- UniProt
- Q0FPQ4
- Ligands
- 0XW, MG, NI, IOD
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mandelate RACEMASE/MUCONATE lactonizing enzyme | protein | 368 | 38% helix, 21% strand | Q0FPQ4 |
| B, C, D, F, G, H | Mandelate RACEMASE/MUCONATE lactonizing enzyme | protein | 367 | 38% helix, 21% strand | Q0FPQ4 |
| E | Mandelate RACEMASE/MUCONATE lactonizing enzyme | protein | 355 | 39% helix, 20% strand | Q0FPQ4 |
Ligands and binding sites
- 0XW · (2S,4R)-4-hydroxy-1,1-dimethylpyrrolidinium-2-carboxylate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- NI · Nickel (II) ion · metal · 2 copies · chains A, C, E, H, B, D, F, G
- IOD · Iodide ion · ion · 61 copies · chains A, C, D, B, F, H, E, G
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 3 copies · chains C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1076 | 0.87 | 0.88 | 138 | IOD, 0XW |
| 2 | 1064 | 0.86 | 0.87 | 121 | IOD, MPD |
| 3 | 887 | 0.85 | 0.87 | 111 | IOD |
| 4 | 685 | 0.83 | 0.87 | 94 | IOD |
| 5 | 278 | 0.73 | 0.87 | 35 | empty |
Interfaces
20 interfaces between chains.
- C–G · 1300 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 1293 Ų buried · 19 hydrogen bonds · protein-protein
- F–H · 1289 Ų buried · 16 hydrogen bonds · protein-protein
- B–E · 1251 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 876 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 4H2H · Crystal structure of an enolase (mandalate racemase subgroup, target EFI-502101) from… · the same entry in another collection · chain H against H, TM-score 1.00
- Q0FPQ4 · AlphaFold monomer V2.0 prediction for 4-hydroxyproline betaine 2-epimerase (Q0FPQ4) · a predicted model of the same protein · chain B 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 Q0FPQ4
- Elsewhere: RCSB PDB 4H2H · PDBe 4H2H · UniProt Q0FPQ4
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