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Crystal structure of mannonate dehydratase PRK15072 (target efi- 502214) from caulobacter sp. K31
Analyse Crystal structure of mannonate dehydratase PRK15072 (target efi- 502214) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4FI4
- Type
- protein
- Length
- 1,213 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mandelate RACEMASE/MUCONATE lactonizing protein
- UniProt
- B0T0B1
- Ligands
- UNL, MG, CL
- Pockets
- 6 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mandelate RACEMASE/MUCONATE lactonizing protein | protein | 407 | 38% helix, 19% strand | B0T0B1 |
| B, C | Mandelate RACEMASE/MUCONATE lactonizing protein | protein | 403 | 37% helix, 20% strand | B0T0B1 |
Ligands and binding sites
- UNL · Unknown ligand · ligand · chains C
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
- CL · Chloride ion · ion · 5 copies · chains A, B, C
- GOL · Glycerol · additive · 12 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 349 | 0.65 | 0.80 | 42 | GOL |
| 2 | 363 | 0.65 | 0.80 | 42 | GOL |
| 3 | 339 | 0.64 | 0.80 | 45 | GOL |
| 4 | 350 | 0.57 | 0.75 | 47 | GOL |
| 5 | 267 | 0.56 | 0.77 | 33 | CL |
Interfaces
2 interfaces between chains.
- A–C · 356 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 336 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4FI4 · Crystal structure of mannonate dehydratase PRK15072 (TARGET EFI-502214) from Caulobacter… · the same entry in another collection · chain C against C, TM-score 1.00
- B0T0B1 · AlphaFold monomer V2.0 prediction for D-mannonate dehydratase CAUL1427 (B0T0B1) · 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 B0T0B1
- Elsewhere: RCSB PDB 4FI4 · PDBe 4FI4 · UniProt B0T0B1
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