9NBY
AMC008 v4.2 SOSIP Env trimer in complex with PGT121, VRC01 and 3BC315 Fabs
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, E, K (G, K, Q) | PGT121 Fab light chain | polymer | 211 | 22574.9 | 3 | Homo sapiens (human) | ||
| 2 | B, F, L (H, L, R) | PGT121 Fab heavy chain | polymer | 235 | 25169.2 | 3 | Homo sapiens (human) | ||
| 3 | C, G, J (I, M, P) | VRC01 Fab heavy chain | polymer | 224 | 24395.7 | 3 | Homo sapiens (human) | ||
| 4 | D, H, I (J, N, O) | VRC01 Fab light chain | polymer | 210 | 23172.7 | 3 | Homo sapiens (human) | ||
| 5 | M (S) | 3BC315 Fab heavy chain | polymer | 232 | 24999.2 | 1 | Homo sapiens (human) | ||
| 6 | N (T) | 3BC315 Fab light chain | polymer | 216 | 23009.6 | 1 | Homo sapiens (human) | ||
| 7 | O, Q, S (E, A, C) | Envelope glycoprotein gp120 | polymer | 488 | 55212.5 | 3 | Human immunodeficiency virus 1 | ||
| 8 | P, R, T (F, B, D) | Envelope glycoprotein gp41 | polymer | 154 | 17428.8 | 3 | UniProt (Q1AII4) | Human immunodeficiency virus 1 | |
| 9 | AA, AB, BB, DA, DB... (a, 0, 1, d, 3...) | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 424.4 | 39 | In PDB GlyTouCan (G42666HT) | |||
| 10 | BA, EA, GB, HB, W... (b, e, 6, 7, W...) | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 586.5 | 6 | In PDB GlyTouCan (G15407YE) | |||
| 11 | CA (c) | alpha-D-mannopyranose-(1-3)-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 | 1073.0 | 1 | In PDB GlyTouCan (G09724ZC) | |||
| 12 | FA, NB, UA (f, DA, u) | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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 | 1559.4 | 3 | In PDB GlyTouCan (G68668TB) | |||
| 13 | CB, NA (2, n) | 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 | 2 | In PDB GlyTouCan (G94106MV) | |||
| 14 | OA (o) | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 732.7 | 1 | In PDB GlyTouCan (G32152BH) | |||
| 15 | RA (r) | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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 | 1 | In PDB GlyTouCan (G56014GC) | |||
| 16 | IB (8) | alpha-D-mannopyranose-(1-3)-[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 | 910.8 | 1 | In PDB GlyTouCan (G22768VO) | |||
| 17 | JB (9) | 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 | 1 | In PDB GlyTouCan (G55220VL) | |||
| 18 | AC, BC, CC, DC, EC... (A, B, C, J, E) | 2-acetamido-2-deoxy-beta-D-glucopyranose | non-polymer | 221.2 | 10 | Chemie (NAG) |
Sequence modifications
F, B, D: 512 - 664 (UniProt: Q1AII4)
| PDB | External Database | Details |
|---|---|---|
| Thr 514 | Ala 4 | conflict |
| Asn 543 | Gln 33 | conflict |
| Pro 559 | Ile 49 | conflict |
| Cys 605 | Thr 95 | conflict |
| Ser 607 | Ala 97 | conflict |
| Thr 612 | Ala 102 | conflict |
| Leu 646 | Ile 136 | conflict |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 20 |
| Total formula weight | 551870.5 | |
| Branched | Number of molecules | 55 |
| Total formula weight | 31919.5 | |
| Non-Polymers* | Number of molecules | 10 |
| Total formula weight | 2212.1 | |
| All* | Total formula weight | 586002.1 |
