MolNFT v1 · #54093 · protein
Nocardia farcinica maleate cis-trans isomerase C194S mutant with a covalently bound succinylcysteine intermediate
2XED · Putative maleate isomerase: “Nocardia farcinica maleate cis-trans isomerase C194S mutant with a covalently bound succinylcysteine…”. X-ray diffraction, 7 pockets (best druggability 0.58). MolNFT v1 #54093 on GenesisL1: 3D structure…
- PDB
- 2XED
- Type
- protein
- Length
- 988 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative maleate isomerase
- EC
- 5.2.1.1
- UniProt
- Q5YXQ1
- Pockets
- 7 · best druggability 0.58
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative maleate isomerase (EC 5.2.1.1) | protein | 252 | 44% helix, 19% strand | Q5YXQ1 |
| B | Putative maleate isomerase (EC 5.2.1.1) | protein | 246 | 45% helix, 20% strand | Q5YXQ1 |
| C, D | Putative maleate isomerase (EC 5.2.1.1) | protein | 245 | 45% helix, 19% strand | Q5YXQ1 |
Ligands and binding sites
- SIN · Succinic acid · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 239 | 0.58 | 0.79 | 31 | empty |
| 2 | 343 | 0.55 | 0.75 | 41 | empty |
| 3 | 73 | 0.34 | 0.76 | 13 | empty |
| 4 | 57 | 0.29 | 0.74 | 9 | empty |
| 5 | 64 | 0.28 | 0.73 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–D · 949 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 438 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 384 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (additive adduct).
Compared structures
- 2XED · Nocardia farcinica maleate cis-trans isomerase C194S mutant with a covalently bound… · the same entry in another collection · chain A against A, TM-score 1.00
- Q5YXQ1 · AlphaFold monomer V2.0 prediction for maleate isomerase (Q5YXQ1) · 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 Q5YXQ1
- Elsewhere: RCSB PDB 2XED · PDBe 2XED · UniProt Q5YXQ1
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