9BER
Cryo-EM structure of the HIV-1 JR-FL IDL Env trimer in complex with PGT122 Fab
Entity
Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
1 | G, A, F | Envelope glycoprotein gp120 | polymer | 477 | 53686.9 | 3 | UniProt (Q75760) In PDB | Human immunodeficiency virus 1 (HIV-1) | |
2 | B, C, I | Envelope glycoprotein gp41 | polymer | 153 | 17227.5 | 3 | UniProt (Q6BC19) In PDB | Human immunodeficiency virus 1 (HIV-1) | |
3 | H, D, J | PGT122 heavy chain | polymer | 132 | 14838.7 | 3 | Homo sapiens (human) | ||
4 | L, E, K | PGT122 light chain | polymer | 105 | 11423.5 | 3 | Homo sapiens (human) | ||
5 | b, c, M, N, P... | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 424.4 | 12 | In PDB GlyTouCan (G42666HT) | |||
6 | a, O, U | 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) | |||
7 | d, R, X | 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 | 3 | In PDB GlyTouCan (G09724ZC) | |||
8 | A, G, C, F, B... | 2-acetamido-2-deoxy-beta-D-glucopyranose | non-polymer | 221.2 | 45 | Chemie (NAG) | |||
9 | A | SULFATE ION | non-polymer | 96.1 | 1 | Chemie (SO4) |
Sequence modifications
G, A, F: 31 - 505 (UniProt: Q75760)
B, C, I: 512 - 664 (UniProt: Q6BC19)
PDB | External Database | Details |
---|---|---|
Cys 113 | Asp 112 | conflict |
Lys 168 | Glu 165 | conflict |
Asn 197 | Asp 194 | conflict |
Thr 236 | Lys 233 | conflict |
Gly 431 | - | insertion |
Cys 431 | - | insertion |
Gly 432 | Lys 423 | conflict |
Val 506 | - | expression tag |
Gly 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 |
---|---|---|
Pro 559 | Ile 550 | conflict |
Sequence viewer
Contents of the asymmetric unit
Polymers | Number of chains | 12 |
Total formula weight | 291530.2 | |
Branched | Number of molecules | 18 |
Total formula weight | 10557.8 | |
Non-Polymers* | Number of molecules | 46 |
Total formula weight | 10050.4 | |
All* | Total formula weight | 312138.4 |