Research workbench
Matc (RPA3494) from rhodopseudomonas palustris with bound malate
Analyse Matc (RPA3494) from rhodopseudomonas palustris with bound malate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HKE
- Type
- protein
- Length
- 885 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Possible tctc subunit of the tripartite tricarboxylate TRANSPORT(TTT) family
- UniProt
- Q6N446
- Ligands
- MLT, LMR
- Pockets
- 7 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Possible tctc subunit of the tripartite tricarboxylate TRANSPORT(TTT) family | protein | 294 | 42% helix, 21% strand | Q6N446 |
| B | Possible tctc subunit of the tripartite tricarboxylate TRANSPORT(TTT) family | protein | 296 | 43% helix, 21% strand | Q6N446 |
| C | Possible tctc subunit of the tripartite tricarboxylate TRANSPORT(TTT) family | protein | 295 | 43% helix, 21% strand | Q6N446 |
Ligands and binding sites
- MLT · D-malate · ligand · 3 copies · chains A, B, C
- LMR · (2S)-2-hydroxybutanedioic acid · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 402 | 0.70 | 0.82 | 58 | empty |
| 2 | 478 | 0.61 | 0.75 | 50 | empty |
| 3 | 69 | 0.51 | 0.85 | 18 | empty |
| 4 | 102 | 0.51 | 0.82 | 23 | empty |
| 5 | 90 | 0.47 | 0.81 | 24 | empty |
Interfaces
2 interfaces between chains.
- A–B · 792 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 460 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6HKE · MatC (Rpa3494) from Rhodopseudomonas palustris with bound 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 Q6N446
- Elsewhere: RCSB PDB 6HKE · PDBe 6HKE · UniProt Q6N446
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.