9BDT
Apolipoprotein B 100 bound to LDL receptor and legobody
This is a non-PDB format compatible entry.
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | A (A) | Apolipoprotein B-100 | polymer | 4563 | 516167.5 | 1 | UniProt (P04114) Pfam (PF01347) Pfam (PF09172) Pfam (PF06448) Pfam (PF12491) | Homo sapiens (human) | Apo B-48 |
| 2 | B (H) | Legobody 8D3 Fab Heavy Chain | polymer | 234 | 25252.2 | 1 | Mus musculus | ||
| 3 | C (L) | Legobody 8D3 Fab Light Chain | polymer | 219 | 24095.9 | 1 | Mus musculus | ||
| 4 | D (B) | Maltodextrin-binding protein,Immunoglobulin G-binding protein A,Immunoglobulin G-binding protein G | polymer | 545 | 59233.2 | 1 | UniProt (C3SHQ8) UniProt (P99134) UniProt (P06654) Pfam (PF01547) Pfam (PF02216) Pfam (PF01378) UniProt (by SIFTS) (P0AEX9) UniProt (by SIFTS) (P02976) | Escherichia coli | IgG-binding protein A,Staphylococcal protein A,SpA,IgG-binding protein G |
| 5 | E, G (I, R) | Low-density lipoprotein receptor | polymer | 860 | 95477.0 | 2 | UniProt (P01130) Pfam (PF00057) Pfam (PF00058) Pfam (PF14670) | Homo sapiens (human) | LDL receptor |
| 6 | F (N) | ApoB100 nanobody 4 | polymer | 131 | 14322.9 | 1 | Camelus bactrianus | ||
| 7 | H (G) | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 424.4 | 1 | In PDB GlyTouCan (G42666HT) | |||
| 8 | I, J, K, L (A) | 2-acetamido-2-deoxy-beta-D-glucopyranose | non-polymer | 221.2 | 4 | Chemie (NAG) | |||
| 9 | M, N, O, P, Q... (R) | CALCIUM ION | non-polymer | 40.1 | 7 | Chemie (CA) |
Sequence modifications
B: 3 - 360 (UniProt: C3SHQ8)
B: 361 - 468 (UniProt: P99134)
B: 480 - 537 (UniProt: P06654)
| PDB | External Database | Details |
|---|---|---|
| Met 2 | - | initiating methionine |
| PDB | External Database | Details |
|---|---|---|
| Ala 362 | Gln 44 | conflict |
| Leu 363 | Asn 45 | conflict |
| Ala 366 | Tyr 48 | conflict |
| Ile 368 | Val 50 | conflict |
| Ile 370 | Asn 52 | conflict |
| Thr 375 | Asn 57 | conflict |
| Glu 376 | Ala 58 | conflict |
| Glu 377 | Asp 59 | conflict |
| Val 392 | Gln 74 | conflict |
| Lys 394 | Ala 76 | conflict |
| Glu 395 | Asn 77 | conflict |
| Ile 396 | Val 78 | conflict |
| Ala 398 | Gly 80 | conflict |
| Lys 401 | Gln 83 | conflict |
| Glu 405 | Asp 87 | conflict |
| His 406 | Ser 88 | conflict |
| - | Ala 93 | deletion |
| Gly 411 | Asp 94 | conflict |
| Gly 412 | Ala 95 | conflict |
| Ser 413 | Gln 96 | conflict |
| Gly 414 | Gln 97 | conflict |
| Gly 415 | Asn 98 | conflict |
| Ala 416 | Asn 99 | conflict |
| Gly 417 | Phe 100 | conflict |
| Ser 418 | Asn 101 | conflict |
| Gly 419 | Lys 102 | conflict |
| Gly 469 | - | linker |
| Gly 470 | - | linker |
| Gly 471 | - | linker |
| Ser 472 | - | linker |
| Gly 473 | - | linker |
| Gly 474 | - | linker |
| Gly 475 | - | linker |
| Ser 476 | - | linker |
| Gly 477 | - | linker |
| Gly 478 | - | linker |
| Ser 479 | - | linker |
| PDB | External Database | Details |
|---|---|---|
| Gly 538 | - | expression tag |
| Ser 539 | - | expression tag |
| Gly 540 | - | expression tag |
| His 541 | - | expression tag |
| His 542 | - | expression tag |
| His 543 | - | expression tag |
| His 544 | - | expression tag |
| His 545 | - | expression tag |
| His 546 | - | expression tag |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 7 |
| Total formula weight | 830025.7 | |
| Branched | Number of molecules | 1 |
| Total formula weight | 424.4 | |
| Non-Polymers* | Number of molecules | 11 |
| Total formula weight | 1165.4 | |
| All* | Total formula weight | 831615.5 |
