MolNFT v1 · #154986 · protein
Crystal structure of sure with D-leu
6KSV · ALPHA/BETA hydrolase: “Crystal structure of sure with D-leu”. X-ray diffraction, 4 ligands (DLE, E7L, YT3), 5 pockets (best druggability 0.83). MolNFT v1 #154986 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6KSV
- Type
- protein
- Length
- 853 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ALPHA/BETA hydrolase
- UniProt
- A0A4Q6RSJ1
- Ligands
- DLE, E7L, YT3, SO4
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ALPHA/BETA hydrolase | protein | 427 | 31% helix, 24% strand | A0A4Q6RSJ1 |
| B | ALPHA/BETA hydrolase | protein | 426 | 31% helix, 24% strand | A0A4Q6RSJ1 |
Ligands and binding sites
- DLE · D-leucine · ligand · chains A
- E7L · S-(2-acetamidoethyl) (2R)-2-azanyl-4-methyl-pentanethioate · ligand · chains B
- YT3 · Yttrium (III) ion · metal · 3 copies · chains A, B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 554 | 0.83 | 0.89 | 77 | empty |
| 2 | 392 | 0.58 | 0.75 | 52 | empty |
| 3 | 264 | 0.51 | 0.75 | 31 | DLE |
| 4 | 221 | 0.47 | 0.74 | 28 | E7L |
| 5 | 87 | 0.44 | 0.79 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1086 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6KSV · Crystal structure of SurE with D-Leu · 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 A0A4Q6RSJ1
- Elsewhere: RCSB PDB 6KSV · PDBe 6KSV · UniProt A0A4Q6RSJ1
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