9D1W
Cryo-EM structure of PGDM1400 Fab bound to HIV-1 BG505 DS-SOSIP.664 Env trimer
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, B, C (A, B, C) | HIV-1 BG505 DS-SOSIP gp120 | polymer | 481 | 54086.3 | 3 | UniProt (Q2N0S6) Pfam (PF00516) | Human immunodeficiency virus 1 | |
| 2 | D (H) | PGDM1400 heavy chain | polymer | 245 | 26441.6 | 1 | Homo sapiens | ||
| 3 | E (L) | PGDM1400 light chain | polymer | 219 | 24093.7 | 1 | Homo sapiens | ||
| 4 | F, G, H (a, b, c) | HIV-1 BG505 DS-SOSIP glycoprotein gp41 | polymer | 153 | 17146.5 | 3 | UniProt (Q2N0S6) Pfam (PF00517) UniProt (by SIFTS) (D0PUM0) | Human immunodeficiency virus 1 | Env polyprotein |
| 5 | I, R (D, O) | 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 | 2 | In PDB GlyTouCan (G68668TB) | |||
| 6 | AA, BA, CA, DA, EA... (X, Y, Z, d, x...) | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 424.4 | 18 | In PDB GlyTouCan (G42666HT) | |||
| 7 | N (J) | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-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 | 1721.5 | 1 | In PDB GlyTouCan (G89864BN) | |||
| 8 | P, W, Y (M, T, V) | 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 | 3 | In PDB GlyTouCan (G56014GC) | |||
| 9 | X (U) | 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) | |||
| 10 | AB, BB, CB, DB, EB... (C, A, a, b, c...) | 2-acetamido-2-deoxy-beta-D-glucopyranose | non-polymer | 221.2 | 33 | Chemie (NAG) |
Sequence modifications
A, B, C: 31 - 508 (UniProt: Q2N0S6)
a, b, c: 512 - 664 (UniProt: Q2N0S6)
| PDB | External Database | Details |
|---|---|---|
| Cys 201 | Ile 200 | conflict |
| Asn 332 | Thr 330 | conflict |
| Cys 433 | Ala 430 | conflict |
| Cys 501 | Ala 498 | conflict |
| 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 | 8 |
| Total formula weight | 264233.7 | |
| Branched | Number of molecules | 25 |
| Total formula weight | 16285.0 | |
| Non-Polymers* | Number of molecules | 33 |
| Total formula weight | 7299.9 | |
| All* | Total formula weight | 287818.6 |
