MolNFT v1 · #135193 · protein
Crystal structure of the unliganded DH270 cooperating lineage member DH272
5TRP · DH272 Fab heavy chain: “Crystal structure of the unliganded DH270 cooperating lineage member DH272”. X-ray diffraction, 2 ligands (NAG, SO4), 3 pockets (best druggability 0.60). MolNFT v1 #135193 on GenesisL1: 3D structure, binding…
- PDB
- 5TRP
- Type
- protein
- Length
- 439 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DH272 Fab heavy chain; DH272 Fab light chain
- Ligands
- NAG, SO4
- Pockets
- 3 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | DH272 Fab heavy chain | protein | 222 | 4% helix, 53% strand | — |
| L | DH272 Fab light chain | protein | 217 | 5% helix, 52% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains L
- SO4 · Sulfate ion · ion · chains H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 563 | 0.60 | 0.74 | 54 | empty |
| 2 | 94 | 0.37 | 0.75 | 17 | empty |
| 3 | 72 | 0.29 | 0.72 | 15 | empty |
Interfaces
1 interface between chains.
- H–L · 1897 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 5TRP · Crystal Structure of the Unliganded DH270 Cooperating Lineage Member DH272 · the same entry in another collection · chain H against H, 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 5TRP · PDBe 5TRP
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