Research workbench
Crystal structure of muconate cycloisomerase from thermotoga maritima MSB8
Analyse Crystal structure of muconate cycloisomerase from thermotoga maritima MSB8 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ZAD
- Type
- protein
- Length
- 1,376 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Muconate cycloisomerase
- EC
- 5.5.1.1
- UniProt
- Q9WXM1
- Ligands
- MN
- Pockets
- 11 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Muconate cycloisomerase (EC 5.5.1.1) | protein | 344 | 43% helix, 24% strand | Q9WXM1 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
- 1PE · Pentaethylene glycol · additive · 11 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1101 | 0.84 | 0.85 | 88 | empty |
| 2 | 531 | 0.81 | 0.87 | 62 | PEG |
| 3 | 519 | 0.81 | 0.87 | 64 | empty |
| 4 | 377 | 0.74 | 0.85 | 48 | empty |
| 5 | 290 | 0.72 | 0.86 | 35 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1413 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 1399 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 711 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 modified (engineered).
Compared structures
- 2ZAD · Crystal Structure of Muconate Cycloisomerase from Thermotoga maritima MSB8 · the same entry in another collection · chain D against D, TM-score 1.00
- Q9WXM1 · AlphaFold monomer V2.0 prediction for L-ala-D/L-glu epimerase (Q9WXM1) · 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 Q9WXM1
- Elsewhere: RCSB PDB 2ZAD · PDBe 2ZAD · UniProt Q9WXM1
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