Research workbench
Crystal structure of SERBB3-FAB3379 complex
Analyse Crystal structure of SERBB3-FAB3379 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CUS
- Type
- protein
- Length
- 3,646 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Receptor tyrosine-protein kinase erbb-3; IgG H chain; Fab lc region of KTN3379
- EC
- 2.7.10.1
- UniProt
- P21860, S6B291
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.69
Structure
x-ray diffraction · 12 distinct chains · 6% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Receptor tyrosine-protein kinase erbb-3 (EC 2.7.10.1) | protein | 561 | 8% helix, 23% strand | P21860 |
| B | Receptor tyrosine-protein kinase erbb-3 (EC 2.7.10.1) | protein | 530 | 8% helix, 25% strand | P21860 |
| C | Receptor tyrosine-protein kinase erbb-3 (EC 2.7.10.1) | protein | 539 | 6% helix, 19% strand | P21860 |
| D | Receptor tyrosine-protein kinase erbb-3 (EC 2.7.10.1) | protein | 509 | 6% helix, 23% strand | P21860 |
| H | IgG H chain | protein | 182 | 5% helix, 48% strand | S6B291 |
| L | Fab lc region of KTN3379 | protein | 185 | 6% helix, 44% strand | — |
| I | IgG H chain | protein | 198 | 5% helix, 40% strand | S6B291 |
| J | IgG H chain | protein | 175 | 5% helix, 43% strand | S6B291 |
| K | IgG H chain | protein | 180 | 3% helix, 44% strand | S6B291 |
| M | Fab lc region of KTN3379 | protein | 203 | 1% helix, 41% strand | — |
| N | Fab lc region of KTN3379 | protein | 184 | 2% helix, 42% strand | — |
| O | Fab lc region of KTN3379 | protein | 200 | 4% helix, 38% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains A, B, C, D, M
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 349 | 0.69 | 0.82 | 50 | empty |
| 2 | 432 | 0.68 | 0.80 | 44 | empty |
| 3 | 386 | 0.67 | 0.80 | 33 | empty |
| 4 | 55 | 0.67 | 0.96 | 22 | empty |
| 5 | 179 | 0.59 | 0.82 | 24 | empty |
Interfaces
24 interfaces between chains.
- H–L · 1592 Ų buried · 13 hydrogen bonds · protein-protein
- I–M · 1541 Ų buried · 7 hydrogen bonds · protein-protein
- K–O · 1260 Ų buried · 7 hydrogen bonds · protein-protein
- J–N · 1195 Ų buried · 6 hydrogen bonds · protein-protein
- I–K · 853 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 102 disulfide (disulfide).
Compared structures
- 5CUS · Crystal Structure of sErbB3-Fab3379 Complex · the same entry in another collection · chain O against O, 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 P21860
- Every structure of UniProt S6B291
- Elsewhere: RCSB PDB 5CUS · PDBe 5CUS · UniProt P21860 · UniProt S6B291
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