7LY9
Cryo-EM structure of 2909 Fab in complex with 3BNC117 Fab and CAP256.wk34.c80 SOSIP.RnS2 N160K HIV-1 Env trimer
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | A (L) | 2909 Light Chain | polymer | 211 | 22582.9 | 1 | Homo sapiens (Human) | ||
| 2 | B (H) | 2909 Heavy Chain | polymer | 231 | 25067.8 | 1 | Homo sapiens (Human) | ||
| 3 | C, G, K (G, D, K) | Envelope glycoprotein gp120 | polymer | 471 | 53337.5 | 3 | UniProt (A0A0N9FF17) | Human immunodeficiency virus 1 (HIV-1) | |
| 4 | D, H, L (B, E, A) | 3BNC117 Heavy Chain | polymer | 226 | 24656.5 | 3 | Homo sapiens (Human) | ||
| 5 | E, I, M (C, I, M) | 3BNC117 Light Chain | polymer | 206 | 23022.7 | 3 | Homo sapiens (Human) | ||
| 6 | F, J, N (F, J, N) | Envelope glycoprotein gp41 | polymer | 154 | 17355.7 | 3 | UniProt (A0A0N9FF17) UniProt (by SIFTS) (W6HZ60) | Human immunodeficiency virus 1 (HIV-1) | |
| 7 | O, P, S, T, W... (O, P, S, T, W...) | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 424.4 | 7 | In PDB GlyTouCan (G42666HT) | |||
| 8 | Q, U, Z (Q, U, Z) | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 1235.1 | 3 | In PDB GlyTouCan (G55220VL) | |||
| 9 | R (R) | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 748.7 | 1 | In PDB GlyTouCan (G81315DD) | |||
| 10 | V (V) | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 586.5 | 1 | In PDB GlyTouCan (G15407YE) | |||
| 11 | AA, AB, AC, BA, BB... (G, D, N, I, J...) | 2-acetamido-2-deoxy-beta-D-glucopyranose | non-polymer | 221.2 | 54 | Chemie (NAG) |
Sequence modifications
G, D, K: 33 - 500 (UniProt: A0A0N9FF17)
F, J, N: 511 - 664 (UniProt: A0A0N9FF17)
| PDB | External Database | Details |
|---|---|---|
| Lys 160 | Asn 149 | conflict |
| Ile 204 | Ala 196 | conflict |
| Met 302 | Asn 294 | conflict |
| Leu 320 | Thr 310 | conflict |
| Pro 329 | Ala 320 | conflict |
| Pro 437 | Ser 423 | conflict |
| Asn 442 | Glu 428 | conflict |
| Cys 501 | - | expression tag |
| Asn 502 | - | expression tag |
| Arg 503 | - | expression tag |
| Thr 504 | - | expression tag |
| Val 505 | - | expression tag |
| Val 506 | - | expression tag |
| Gln 507 | - | expression tag |
| Arg 508 | - | expression tag |
| Arg 509 | - | expression tag |
| Arg 510 | - | expression tag |
| Arg 511 | - | expression tag |
| Arg 512 | - | expression tag |
| Arg 513 | - | expression tag |
| PDB | External Database | Details |
|---|---|---|
| Asn 535 | Ile 522 | conflict |
| Pro 559 | Ile 546 | conflict |
| Gly 569 | Thr 556 | conflict |
| Phe 573 | Ile 560 | conflict |
| Glu 588 | Lys 575 | conflict |
| Val 589 | Asp 576 | conflict |
| Cys 605 | Thr 592 | conflict |
| Pro 609 | Tyr 596 | conflict |
| Gly 636 | Asp 623 | conflict |
| Phe 651 | Lys 638 | conflict |
| Ile 655 | Ser 642 | conflict |
| Asn 660 | Leu 647 | conflict |
| Thr 662 | Ala 649 | conflict |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 14 |
| Total formula weight | 402767.8 | |
| Branched | Number of molecules | 12 |
| Total formula weight | 8011.3 | |
| Non-Polymers* | Number of molecules | 54 |
| Total formula weight | 11945.2 | |
| All* | Total formula weight | 422724.3 |
