MolNFT v1 · #129851 · protein
Crystal structure of glycopeptide "GVTSAFPDT*RPAP" in complex with scfv-SM3
5OWP · Ig heavy chain V-III region J606,IG lambda-1 chain V region…: “Crystal structure of glycopeptide "GVTSAFPDT*RPAP" in complex with scfv-SM3”. X-ray diffraction, 1 ligand (A2G), 2 pockets (best druggability 0.34). MolNFT v1 #129851 on…
- PDB
- 5OWP
- Type
- protein
- Length
- 234 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ig heavy chain V-III region J606,IG lambda-1 chain V region H2020…
- UniProt
- P01801, P01726
- Ligands
- A2G
- Pockets
- 2 · best druggability 0.34
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Ig heavy chain V-III region J606,IG lambda-1 chain V region H2020 | protein | 226 | 8% helix, 54% strand | P01801, P01726 |
| D | 5,6-dihydro-BENZO[H]CINNOLIN-3-ylamine | protein | 8 | 0% helix, 0% strand | — |
Ligands and binding sites
- A2G · 2-acetamido-2-deoxy-alpha-D-galactopyranose · sugar · chains H, D
- EDO · 1,2-ethanediol · additive · 3 copies · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 100 | 0.34 | 0.73 | 20 | EDO |
| 2 | 71 | 0.30 | 0.74 | 22 | empty |
Interfaces
1 interface between chains.
- H–D · 510 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 1 glycan, 1 modified (disulfide, O-glycosylation, nonstandard).
Compared structures
- 5OWP · Crystal structure of glycopeptide "GVTSAfPDT*RPAP" in complex with scFv-SM3 · the same entry in another collection · chain H against H, TM-score 1.00
- P01801 · AlphaFold monomer V2.0 prediction for ig heavy chain V-III region J606 (P01801) · a predicted model of the same protein · chain H against A, TM-score 0.50
- P01726 · AlphaFold monomer V2.0 prediction for ig lambda-1 chain V region H2020 (P01726) · a predicted model of the same protein · chain H against A, TM-score 0.48
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 P01801
- Every structure of UniProt P01726
- Elsewhere: RCSB PDB 5OWP · PDBe 5OWP · UniProt P01801 · UniProt P01726
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