6E5P
Backbone model based on cryo-EM map at 8.5 A of domain-swapped, glycan-reactive, neutralizing antibody 2G12 bound to HIV-1 Env BG505 DS-SOSIP, which was also bound to CD4-binding site antibody VRC03
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | A, D, N, O, S... (1, 4, K, L, Q...) | 2G12 Light chain | polymer | 212 | 23130.8 | 6 | Homo sapiens | ||
| 2 | B, C, K, P, T... (2, 3, H, M, R...) | 2G12 heavy chain | polymer | 225 | 23932.9 | 6 | Homo sapiens | ||
| 3 | E, G, I (A, C, E) | Envelope glycoprotein gp120 | polymer | 474 | 53086.1 | 3 | UniProt (Q2N0S6) Pfam (PF00516) | Human immunodeficiency virus 1 | |
| 4 | F, H, J (B, D, F) | Envelope glycoprotein gp160 | polymer | 170 | 19102.8 | 3 | UniProt (Q2N0S9) Pfam (PF00517) | Human immunodeficiency virus 1 | |
| 5 | L, Q, W (I, O, V) | VRC03 heavy chain | polymer | 227 | 24699.9 | 3 | Homo sapiens | ||
| 6 | M, R, X (J, P, W) | VRC03 Light chain | polymer | 208 | 23043.7 | 3 | Homo sapiens | ||
| 7 | CA, KA, LA, MA, OA... (Y, g, h, i, k...) | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose | branched | 342.3 | 9 | In PDB BIRD (PRD_900111) GlyTouCan (G53402KW) | 2alpha-alpha-mannobiose | ||
| 8 | AA, NA, QA (U, j, m) | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 1073.0 | 3 | In PDB GlyTouCan (G94106MV) | |||
| 9 | BA, DA, FA, HA, JA... (X, Z, b, d, f...) | alpha-D-mannopyranose-(1-2)-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 | 6 | In PDB GlyTouCan (G92805XC) | |||
| 10 | EA, GA, IA (a, c, e) | 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 | 3 | In PDB GlyTouCan (G81315DD) |
Sequence modifications
A, C, E: 31 - 506 (UniProt: Q2N0S6)
B, D, F: 512 - 664 (UniProt: Q2N0S9)
| PDB | External Database | Details |
|---|---|---|
| Cys 201 | Ile 200 | conflict |
| Asn 332 | Thr 330 | conflict |
| Cys 433 | Ala 430 | conflict |
| Cys 501 | Ala 498 | conflict |
| PDB | External Database | Details |
|---|---|---|
| Pro 559 | Ile 558 | conflict |
| Cys 605 | Thr 604 | conflict |
| Gly 665 | - | expression tag |
| Ser 666 | - | expression tag |
| Ala 667 | - | expression tag |
| Pro 668 | - | expression tag |
| Thr 669 | - | expression tag |
| Lys 670 | - | expression tag |
| Ala 671 | - | expression tag |
| Lys 672 | - | expression tag |
| Arg 673 | - | expression tag |
| Arg 674 | - | expression tag |
| Val 675 | - | expression tag |
| Val 676 | - | expression tag |
| Gln 677 | - | expression tag |
| Arg 678 | - | expression tag |
| Glu 679 | - | expression tag |
| Lys 680 | - | expression tag |
| Arg 681 | - | expression tag |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 24 |
| Total formula weight | 642179.1 | |
| Branched | Number of molecules | 21 |
| Total formula weight | 15956.2 | |
| All* | Total formula weight | 658135.3 |
