MolNFT v1 · #159005 · protein
Crystal structure of anti-GLD52 Fab complex with human GLD52 peptide mimetic
6OBD · Anti-GLD52 Fab light chain: “Crystal structure of anti-GLD52 Fab complex with human GLD52 peptide mimetic”. X-ray diffraction, 2 ligands (OPE, ZN), 10 pockets (best druggability 0.75). MolNFT v1 #159005 on GenesisL1: 3D structure…
- PDB
- 6OBD
- Type
- protein
- Length
- 873 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anti-GLD52 Fab light chain; Anti-GLD52 Fab heavy chain; GLD52 peptide mimetic
- Ligands
- OPE, ZN
- Pockets
- 10 · best druggability 0.75
Structure
x-ray diffraction · 5 distinct chains · 6% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, L | Anti-GLD52 Fab light chain | protein | 216 | 6% helix, 51% strand | — |
| B | Anti-GLD52 Fab heavy chain | protein | 211 | 9% helix, 51% strand | — |
| H | Anti-GLD52 Fab heavy chain | protein | 211 | 6% helix, 51% strand | — |
| E | GLD52 peptide mimetic | protein | 9 | 0% helix, 0% strand | — |
| F | GLD52 peptide mimetic | protein | 10 | 0% helix, 0% strand | — |
Ligands and binding sites
- OPE · Phosphoric acid mono-(2-amino-ethyl) ester · ligand · 2 copies · chains B, E, L, F
- ZN · Zinc ion · metal · 5 copies · chains A, L, B, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 470 | 0.75 | 0.84 | 65 | empty |
| 2 | 388 | 0.72 | 0.83 | 50 | empty |
| 3 | 764 | 0.68 | 0.75 | 84 | empty |
| 4 | 58 | 0.55 | 0.89 | 20 | empty |
| 5 | 206 | 0.47 | 0.75 | 21 | empty |
Interfaces
10 interfaces between chains.
- A–B · 1641 Ų buried · 13 hydrogen bonds · protein-protein
- L–H · 1598 Ų buried · 13 hydrogen bonds · protein-protein
- B–H · 1158 Ų buried · 11 hydrogen bonds · protein-protein
- H–F · 388 Ų buried · 12 hydrogen bonds · protein-protein
- A–L · 385 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 covalent (disulfide, covalent ligand).
Compared structures
- 6OBD · Crystal structure of anti-GLD52 Fab complex with human GLD52 peptide mimetic · 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 6OBD · PDBe 6OBD
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