MolNFT v1 · #85473 · protein
Crystal structures of RV1098C in complex with malate
4ADL · Fumarate hydratase class II: “Crystal structures of RV1098C in complex with malate”. X-ray diffraction, 1 ligand (LMR), 20 pockets (best druggability 0.82). MolNFT v1 #85473 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4ADL
- Type
- protein
- Length
- 1,835 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fumarate hydratase class II
- EC
- 4.2.1.2
- UniProt
- O53446
- Ligands
- LMR
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 62% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Fumarate hydratase class II (EC 4.2.1.2) | protein | 459 | 62% helix, 8% strand | O53446 |
| B | Fumarate hydratase class II (EC 4.2.1.2) | protein | 458 | 62% helix, 8% strand | O53446 |
Ligands and binding sites
- LMR · (2S)-2-hydroxybutanedioic acid · ligand · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 140 | 0.82 | 0.98 | 24 | empty |
| 2 | 142 | 0.79 | 0.97 | 31 | empty |
| 3 | 128 | 0.78 | 0.97 | 28 | empty |
| 4 | 534 | 0.72 | 0.81 | 77 | empty |
| 5 | 70 | 0.71 | 0.97 | 18 | empty |
Interfaces
6 interfaces between chains.
- A–B · 3491 Ų buried · 44 hydrogen bonds · protein-protein
- B–D · 2919 Ų buried · 47 hydrogen bonds · protein-protein
- A–C · 2904 Ų buried · 45 hydrogen bonds · protein-protein
- C–D · 2873 Ų buried · 35 hydrogen bonds · protein-protein
- A–D · 2019 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- 4ADL · Crystal structures of Rv1098c in complex with malate · the same entry in another collection · chain A 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 O53446
- Elsewhere: RCSB PDB 4ADL · PDBe 4ADL · UniProt O53446
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.