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Crystal structure of mandelate RACEMASE/MUCONATE lactonizing protein from herpetosiphon aurantiacus
Analyse Crystal structure of mandelate RACEMASE/MUCONATE lactonizing protein from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IK4
- Type
- protein
- Length
- 1,406 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mandelate RACEMASE/MUCONATE lactonizing protein
- UniProt
- A9B055
- Ligands
- K
- Pockets
- 13 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mandelate RACEMASE/MUCONATE lactonizing protein | protein | 351 | 42% helix, 23% strand | A9B055 |
| B | Mandelate RACEMASE/MUCONATE lactonizing protein | protein | 358 | 41% helix, 25% strand | A9B055 |
| C | Mandelate RACEMASE/MUCONATE lactonizing protein | protein | 349 | 43% helix, 23% strand | A9B055 |
| D | Mandelate RACEMASE/MUCONATE lactonizing protein | protein | 348 | 41% helix, 21% strand | A9B055 |
Ligands and binding sites
- K · Potassium ion · metal · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 140 | 0.79 | 0.96 | 21 | GOL |
| 2 | 986 | 0.77 | 0.79 | 114 | K |
| 3 | 478 | 0.67 | 0.79 | 46 | K |
| 4 | 235 | 0.62 | 0.82 | 29 | empty |
| 5 | 389 | 0.62 | 0.78 | 44 | K |
Interfaces
6 interfaces between chains.
- A–B · 1273 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 381 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 251 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 238 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 143 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3IK4 · CRYSTAL STRUCTURE OF mandelate racemase/muconate lactonizing protein from Herpetosiphon… · the same entry in another collection · chain D against D, TM-score 1.00
- A9B055 · AlphaFold monomer V2.0 prediction for aromatic dipeptide epimerase (A9B055) · a predicted model of the same protein · chain D 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 A9B055
- Elsewhere: RCSB PDB 3IK4 · PDBe 3IK4 · UniProt A9B055
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