MolNFT v1 · #155602 · protein
Crystal structure of 73MUL9 fv-clasp fragment in complex with ga- pyridine analogue
6LCS · Vh-sarah: “Crystal structure of 73MUL9 fv-clasp fragment in complex with ga- pyridine analogue”. X-ray diffraction, 2 ligands (E9R, PO4), 4 pockets (best druggability 0.66). MolNFT v1 #155602 on GenesisL1: 3D structure, binding…
- PDB
- 6LCS
- Type
- protein
- Length
- 329 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vh-sarah; Vl-sarah
- Ligands
- E9R, PO4
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vh-sarah | protein | 168 | 30% helix, 41% strand | — |
| B | Vl-sarah | protein | 161 | 29% helix, 32% strand | — |
Ligands and binding sites
- E9R · (2~{S})-6-[4-(hydroxymethyl)-3-oxidanyl-pyridin-1-ium-1-yl]-2-(phenylmethoxycarbonylamino)hexanoic acid · ligand · chains A, B
- PO4 · Phosphate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 510 | 0.66 | 0.77 | 53 | empty |
| 2 | 52 | 0.47 | 0.84 | 12 | E9R |
| 3 | 55 | 0.34 | 0.78 | 16 | empty |
| 4 | 59 | 0.30 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 2491 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 6LCS · Crystal structure of 73MuL9 Fv-clasp fragment in complex with GA-pyridine analogue · 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
- Elsewhere: RCSB PDB 6LCS · PDBe 6LCS
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