MolNFT v1 · #58411 · protein
Crystal structure of isolated domain III of the extracellular region of the epidermal growth factor receptor in complex with the Fab fragment of imc-11F8
3B2U · Imc-11F8 Fab light chain: “Crystal structure of isolated domain III of the extracellular region of the epidermal growth factor receptor…”. X-ray diffraction, 4 ligands (NAG, BMA, MAN), 20 pockets (best druggability 0.77). MolNFT v1…
- PDB
- 3B2U
- Type
- protein
- Length
- 4,984 residues
- Chains
- 24
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Imc-11F8 Fab light chain; Imc-11F8 Fab heavy chain; Epidermal growth factor receptor
- EC
- 2.7.10.1
- UniProt
- P00533
- Ligands
- NAG, BMA, MAN, SO4
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 10 distinct chains · 10% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, D, G, K, O, R, U, X | Imc-11F8 Fab light chain | protein | 213 | 7% helix, 50% strand | — |
| H, J, Q | Imc-11F8 Fab heavy chain | protein | 217 | 6% helix, 52% strand | — |
| A, M | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 195 | 18% helix, 22% strand | P00533 |
| C | Imc-11F8 Fab heavy chain | protein | 213 | 6% helix, 52% strand | — |
| B, E, S | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 194 | 20% helix, 21% strand | P00533 |
| F | Imc-11F8 Fab heavy chain | protein | 215 | 6% helix, 52% strand | — |
| I, P, V | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 193 | 20% helix, 21% strand | P00533 |
| N | Imc-11F8 Fab heavy chain | protein | 218 | 6% helix, 51% strand | — |
| T | Imc-11F8 Fab heavy chain | protein | 216 | 8% helix, 51% strand | — |
| W | Imc-11F8 Fab heavy chain | protein | 216 | 7% helix, 52% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 50 copies · chains A, B, E, I, H, M, W, P, S, V, J, F, C, T, N
- BMA · beta-D-mannopyranose · sugar · 11 copies · chains A, B, E, I, H, M, W, P, S, V
- MAN · alpha-D-mannopyranose · sugar · 5 copies · chains A, E, I, M
- SO4 · Sulfate ion · ion · 8 copies · chains L, A, G, E, K, O, M, U, X, V
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 589 | 0.77 | 0.83 | 103 | empty |
| 2 | 973 | 0.76 | 0.79 | 103 | empty |
| 3 | 1056 | 0.74 | 0.77 | 86 | empty |
| 4 | 567 | 0.74 | 0.82 | 77 | empty |
| 5 | 472 | 0.73 | 0.83 | 66 | empty |
Interfaces
47 interfaces between chains.
- X–W · 1601 Ų buried · 11 hydrogen bonds · protein-protein
- L–H · 1597 Ų buried · 11 hydrogen bonds · protein-protein
- K–J · 1594 Ų buried · 13 hydrogen bonds · protein-protein
- O–N · 1582 Ų buried · 16 hydrogen bonds · protein-protein
- R–Q · 1568 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 64 disulfide, 32 glycan (disulfide, N-glycosylation).
Compared structures
- 3B2U · Crystal structure of isolated domain III of the extracellular region of the epidermal… · the same entry in another collection · chain J against J, 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
- Every structure of UniProt P00533
- Elsewhere: RCSB PDB 3B2U · PDBe 3B2U · UniProt P00533
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