MolNFT v1 · #95380 · protein
Meditope-enabled trastuzumab in complex with cqfdlstrrlkc
4IOI · Trastuzumab light chain: “Meditope-enabled trastuzumab in complex with cqfdlstrrlkc”. X-ray diffraction, 7 pockets (best druggability 0.60). MolNFT v1 #95380 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4IOI
- Type
- protein
- Length
- 562 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trastuzumab light chain; Trastuzumab heavy chain; Immunoglobulin G-binding protein a…
- UniProt
- P0A015, Q51918
- Pockets
- 7 · best druggability 0.60
Structure
x-ray diffraction · 5 distinct chains · 17% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Trastuzumab light chain | protein | 214 | 6% helix, 51% strand | — |
| B | Trastuzumab heavy chain | protein | 220 | 10% helix, 54% strand | — |
| H | Immunoglobulin G-binding protein a | protein | 53 | 79% helix, 0% strand | P0A015 |
| E | Protein L | protein | 63 | 30% helix, 44% strand | Q51918 |
| C | Meditope | protein | 12 | 0% helix, 50% strand | — |
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 415 | 0.60 | 0.76 | 50 | empty |
| 2 | 316 | 0.55 | 0.75 | 43 | empty |
| 3 | 180 | 0.44 | 0.74 | 29 | empty |
| 4 | 145 | 0.43 | 0.75 | 23 | empty |
| 5 | 126 | 0.41 | 0.76 | 20 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1874 Ų buried · 15 hydrogen bonds · protein-protein
- A–E · 688 Ų buried · 11 hydrogen bonds · protein-protein
- B–H · 592 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 512 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 422 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 4IOI · Meditope-enabled trastuzumab in complex with CQFDLSTRRLKC · the same entry in another collection · chain A against A, TM-score 1.00
- P0A015 · AlphaFold monomer V2.0 prediction for immunoglobulin G-binding protein a (P0A015) · a predicted model of the same protein · chain H against A, TM-score 0.92
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 P0A015
- Every structure of UniProt Q51918
- Elsewhere: RCSB PDB 4IOI · PDBe 4IOI · UniProt P0A015 · UniProt Q51918
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