MolNFT v1 · #61212 · protein
Crystal structure of dipeptide epimerase from thermotoga maritima complexed with L-ala-L-lys dipeptide
3DER · Muconate cycloisomerase: “Crystal structure of dipeptide epimerase from thermotoga maritima complexed with L-ala-L-lys dipeptide”. X-ray diffraction, 1 ligand (MG), 16 pockets (best druggability 0.86). MolNFT v1 #61212 on GenesisL1…
- PDB
- 3DER
- Type
- protein
- Length
- 1,372 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Muconate cycloisomerase
- UniProt
- Q9WXM1
- Ligands
- MG
- Pockets
- 16 · best druggability 0.86
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 | protein | 343 | 43% helix, 24% strand | Q9WXM1 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 833 | 0.86 | 0.89 | 96 | empty |
| 2 | 411 | 0.82 | 0.90 | 47 | empty |
| 3 | 439 | 0.81 | 0.89 | 47 | empty |
| 4 | 167 | 0.60 | 0.83 | 24 | empty |
| 5 | 249 | 0.58 | 0.79 | 25 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1392 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 1025 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 1023 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 517 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 506 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3DER · Crystal structure of dipeptide epimerase from Thermotoga maritima complexed with… · 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 C 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 3DER · PDBe 3DER · UniProt Q9WXM1
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