5V7J
Crystal Structure at 3.7 A Resolution of Glycosylated HIV-1 Clade A BG505 SOSIP.664 Prefusion Env Trimer with Four Glycans (N197, N276, N362, and N462) removed in Complex with Neutralizing Antibodies 3H+109L and 35O22.
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | G | Envelope glycoprotein gp160 | polymer | 480 | 53901.1 | 1 | UniProt (Q2N0S6) Pfam (PF00516) In PDB | Human immunodeficiency virus 1 | |
| 2 | B | Envelope glycoprotein gp160 | polymer | 153 | 17146.5 | 1 | UniProt (Q2N0S6) Pfam (PF00517) In PDB | Human immunodeficiency virus 1 | |
| 3 | L | Antibody 3H+109L Fab light chain | polymer | 218 | 23427.0 | 1 | Homo sapiens | ||
| 4 | H | Antibody 3H+109L Fab heavy chain | polymer | 236 | 25339.4 | 1 | Homo sapiens | ||
| 5 | D | Antibody 35O22 Fab light chain | polymer | 240 | 25783.1 | 1 | Homo sapiens | ||
| 6 | E | Antibody 35O22 Fab heavy chain | polymer | 216 | 23318.8 | 1 | Homo sapiens | ||
| 7 | A | 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) | |||
| 8 | C | 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) | |||
| 9 | F, K | alpha-D-mannopyranose-(1-2)-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 | 1235.1 | 2 | In PDB GlyTouCan (G46836GH) | |||
| 10 | I, S | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 586.5 | 2 | In PDB GlyTouCan (G15407YE) | |||
| 11 | J, M | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-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 | 1397.2 | 2 | In PDB GlyTouCan (G81980VO) | |||
| 12 | N | 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 (G47410OF) | |||
| 13 | O | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[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 | 1721.5 | 1 | In PDB GlyTouCan (G40702WU) | |||
| 14 | P | alpha-D-mannopyranose-(1-2)-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 | 1235.1 | 1 | In PDB GlyTouCan (G16404YH) | |||
| 15 | Q, R | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 424.4 | 2 | In PDB GlyTouCan (G42666HT) | |||
| 16 | G, B | 2-acetamido-2-deoxy-beta-D-glucopyranose | non-polymer | 221.2 | 3 | Chemie (NAG) |
Sequence modifications
G: 32 - 508 (UniProt: Q2N0S6)
B: 512 - 664 (UniProt: Q2N0S6)
| PDB | External Database | Details |
|---|---|---|
| Ala 199 | Ser 198 | engineered mutation |
| Ala 278 | Thr 277 | engineered mutation |
| Asn 332 | Thr 330 | engineered mutation |
| Ala 365 | Ser 363 | engineered mutation |
| Ala 464 | Thr 461 | engineered mutation |
| Cys 501 | Ala 498 | engineered mutation |
| Arg 509 | - | expression tag |
| Arg 510 | - | expression tag |
| Arg 511 | - | expression tag |
| Arg 512 | - | expression tag |
| Arg 513 | - | expression tag |
| PDB | External Database | Details |
|---|---|---|
| Pro 559 | Ile 556 | engineered mutation |
| Cys 605 | Thr 602 | engineered mutation |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 6 |
| Total formula weight | 168915.9 | |
| Branched | Number of molecules | 13 |
| Total formula weight | 13624.3 | |
| Non-Polymers* | Number of molecules | 3 |
| Total formula weight | 663.6 | |
| All* | Total formula weight | 183203.8 |
