Nanobody EgB4 bound to the full extracellular EGFR-EGF complex. Determined by X-ray diffraction at 6.05 Å resolution. Released 2 Mar 2022.
Explore 7OM4 in 3D Show helices and sheets RCSB PDB PDBe
7OM4 contains 29 α-helices and 84 β-strands across 3 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 6-7 | 2 | 1 |
| α-helix | 20-31 | 12 | |
| β-strand | 36-37 | 2 | 1 |
| β-strand | 41-44 | 4 | 2 |
| α-helix | 53-57 | 5 | |
| β-strand | 60-61 | 2 | 1 |
| β-strand | 65-68 | 4 | 2 |
| β-strand | 74 | 1 | 3 |
| β-strand | 82-83 | 2 | 1 |
| β-strand | 89 | 1 | 2 |
| β-strand | 93-98 | 6 | 2 |
| β-strand | 110 | 1 | 3 |
| β-strand | 118-119 | 2 | 1 |
| β-strand | 123-127 | 5 | 2 |
| α-helix | 135-137 | 3 | |
| α-helix | 140-142 | 3 | |
| β-strand | 144 | 1 | 1 |
| α-helix | 146-148 | 3 | |
| β-strand | 153 | 1 | 2 |
| α-helix | 171-173 | 3 | |
| β-strand | 175 | 1 | 4 |
| β-strand | 183 | 1 | 4 |
| β-strand | 199 | 1 | 5 |
| α-helix | 204-206 | 3 | |
| β-strand | 207 | 1 | 5 |
| β-strand | 212 | 1 | 6 |
| β-strand | 216 | 1 | 7 |
| α-helix | 221-223 | 3 | |
| β-strand | 224 | 1 | 7 |
| β-strand | 227 | 1 | 6 |
| β-strand | 230-232 | 3 | 8 |
| β-strand | 235-237 | 3 | 8 |
| α-helix | 240-242 | 3 | |
| β-strand | 244-247 | 4 | 9 |
| β-strand | 252-255 | 4 | 9 |
| β-strand | 261-263 | 3 | 10 |
| β-strand | 266-268 | 3 | 10 |
| β-strand | 276-277 | 2 | 11 |
| β-strand | 283-284 | 2 | 11 |
| β-strand | 291 | 1 | 12 |
| β-strand | 294-295 | 2 | 13 |
| β-strand | 300-301 | 2 | 13 |
| α-helix | 303 | 1 | |
| β-strand | 304 | 1 | 12 |
| α-helix | 305-306 | 2 | |
| β-strand | 313-314 | 2 | 14 |
| β-strand | 316 | 1 | 15 |
| α-helix | 319-321 | 3 | |
| α-helix | 331-333 | 3 | |
| β-strand | 340-342 | 3 | 14 |
| β-strand | 344 | 1 | 15 |
| β-strand | 345-347 | 3 | 16 |
| α-helix | 349-353 | 5 | |
| β-strand | 355 | 1 | 17 |
| β-strand | 360 | 1 | 17 |
| α-helix | 361-364 | 4 | |
| α-helix | 365-372 | 8 | |
| β-strand | 376-377 | 2 | 14 |
| β-strand | 381-383 | 3 | 16 |
| β-strand | 392 | 1 | 18 |
| α-helix | 394-396 | 3 | |
| β-strand | 401-402 | 2 | 14 |
| β-strand | 408 | 1 | 16 |
| β-strand | 412-416 | 5 | 16 |
| β-strand | 423 | 1 | 18 |
| β-strand | 431 | 1 | 14 |
| β-strand | 432 | 1 | 19 |
| β-strand | 436-439 | 4 | 16 |
| α-helix | 448-450 | 3 | |
| α-helix | 453-456 | 4 | |
| β-strand | 457 | 1 | 19 |
| β-strand | 464-466 | 3 | 16 |
| α-helix | 472-477 | 6 | |
| β-strand | 486 | 1 | 20 |
| β-strand | 491 | 1 | 21 |
| α-helix | 496-498 | 3 | |
| β-strand | 499 | 1 | 21 |
| β-strand | 502 | 1 | 20 |
| β-strand | 505-507 | 3 | 22 |
| β-strand | 510-512 | 3 | 22 |
| β-strand | 524-527 | 4 | 22 |
| β-strand | 530-533 | 4 | 22 |
| α-helix | 534-535 | 2 | |
| β-strand | 538 | 1 | 23 |
| β-strand | 547 | 1 | 24 |
| α-helix | 552-554 | 3 | |
| β-strand | 555 | 1 | 24 |
| β-strand | 558 | 1 | 23 |
| β-strand | 585-586 | 2 | 25 |
| β-strand | 594-595 | 2 | 25 |
| α-helix | 596-597 | 2 | |
| α-helix | 609-611 | 3 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 3-7 | 5 | 28 |
| β-strand | 11-12 | 2 | 29 |
| β-strand | 18-25 | 8 | 28 |
| α-helix | 29-31 | 3 | |
| β-strand | 33-39 | 7 | 30 |
| β-strand | 46-51 | 6 | 30 |
| β-strand | 57-59 | 3 | 30 |
| β-strand | 64 | 1 | 28 |
| β-strand | 67-72 | 6 | 28 |
| β-strand | 77-82 | 6 | 28 |
| α-helix | 87-89 | 3 | |
| β-strand | 91-98 | 8 | 30 |
| α-helix | 106-108 | 3 | |
| β-strand | 111-112 | 2 | 30 |
| β-strand | 116-118 | 3 | 30 |
| β-strand | 119-120 | 2 | 29 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 20-23 | 4 | 26 |
| β-strand | 28-31 | 4 | 26 |
| α-helix | 33-34 | 2 | |
| β-strand | 37-38 | 2 | 27 |
| β-strand | 44-45 | 2 | 27 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Epidermal growth factor receptor | A | protein | 630 | Homo sapiens | P00533 (AlphaFold model) |
| Epidermal growth factor | C | protein | 53 | Homo sapiens | P01133 (AlphaFold model) |
| Nanobody EgB4 | B | protein | 130 | Lama glama |
>7OM4_1 Epidermal growth factor receptor (chains A) LEEKKVCQGTSNKLTQLGTFEDHFLSLQRMFNNCEVVLGNLEITYVQRNYDLSFLKTIQE VAGYVLIALNTVERIPLENLQIIRGNMYYENSYALAVLSNYDANKTGLKELPMRNLQEIL HGAVRFSNNPALCNVESIQWRDIVSSDFLSNMSMDFQNHLGSCQKCDPSCPNGSCWGAGE ENCQKLTKIICAQQCSGRCRGKSPSDCCHNQCAAGCTGPRESDCLVCRKFRDEATCKDTC PPLMLYNPTTYQMDVNPEGKYSFGATCVKKCPRNYVVTDHGSCVRACGADSYEMEEDGVR KCKKCEGPCRKVCNGIGIGEFKDSLSINATNIKHFKNCTSISGDLHILPVAFRGDSFTHT PPLDPQELDILKTVKEITGFLLIQAWPENRTDLHAFENLEIIRGRTKQHGQFSLAVVSLN ITSLGLRSLKEISDGDVIISGNKNLCYANTINWKKLFGTSGQKTKIISNRGENSCKATGQ VCHALCSPEGCWGPEPRDCVSCRNVSRGRECVDKCNLLEGEPREFVENSECIQCHPECLP QAMNITCTGRGPDNCIQCAHYIDGPHCVKTCPAGVMGENNTLVWKYADAGHVCHLCHPNC TYGCTGPGLEGCPTNGPKIPSAAAHHHHHH
>7OM4_2 Epidermal growth factor (chains C) NSDSECPLSHDGYCLHDGVCMYIEALDKYACNCVVGYIGERCQYRDLKWWELR
>7OM4_3 Nanobody EgB4 (chains B) QVQLQESGGGSVQAGGSLKLSCAASGRSFSTYAMGWFRQAPGQDREFVATISWTDSTDYA DSVKGRFTISRDNAKNTGYLQMNSLKPEDTAVYYCAADRWASSRRNVDYDYWGQGTQVTV SSHGSGLVPR
| ID | Name | Formula | Copies |
|---|---|---|---|
| NAG | 2-acetamido-2-deoxy-beta-D-glucopyranose | C8 H15 N O6 | 7 |
Structural insights into the non-inhibitory mechanism of the anti-EGFR EgB4 nanobody. Zeronian, M.R., Doulkeridou, S., van Bergen En Henegouwen, P.M.P. et al. BMC Mol Cell Biol (2022) 23:12-12. DOI 10.1186/s12860-022-00412-x · PubMed
Other PDB entries of the same protein (UniProt P00533 (AlphaFold model), which also has an AlphaFold model), best resolution first:
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