4R2G
Crystal Structure of PGT124 Fab bound to HIV-1 JRCSF gp120 core and to CD4
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | A, N, O, P (E, O, A, K) | Surface protein gp160 | polymer | 309 | 34754.5 | 4 | UniProt (P20871) Pfam (PF00516) | Human immunodeficiency virus type 1 group M subtype B (HIV-1) | Env polyprotein,Env polyprotein |
| 2 | B, E, H, K (F, B, H, L) | T-cell surface glycoprotein CD4 | polymer | 184 | 20419.3 | 4 | UniProt (P01730) Pfam (PF00047) Pfam (PF05790) | Homo sapiens (Human) | T-cell surface antigen T4/Leu-3 |
| 3 | C, F, I, L (P, C, I, M) | PGT124 Light Chain | polymer | 214 | 23056.6 | 4 | UniProt (P0DOY3) Pfam (PF07654) | Homo sapiens (human) | Ig lambda chain C region DOT,Ig lambda chain C region NEWM,Ig lambda-3 chain C regions |
| 4 | D, G, J, M (Q, D, J, N) | PGT124 Heavy Chain | polymer | 236 | 25460.5 | 4 | UniProt (P0DOX5) Pfam (PF07686) Pfam (PF07654) | Homo sapiens (human) | Immunoglobulin gamma-1 heavy chain NIE |
| 5 | Q, R, S, V (G, R, S, V) | 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 | 4 | In PDB GlyTouCan (G40702WU) | |||
| 6 | T, U (T, U) | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 424.4 | 2 | In PDB GlyTouCan (G42666HT) | |||
| 7 | AA, AB, BA, BB, CA... (E, K, O, A) | 2-acetamido-2-deoxy-beta-D-glucopyranose | non-polymer | 221.2 | 26 | Chemie (NAG) | |||
| 8 | DB, EA, QA, XA (K, E, O, A) | CHLORIDE ION | non-polymer | 35.5 | 4 | Chemie (CL) | |||
| 9 | FA, GA, HA, IA (Q, D, J, N) | GLYCEROL | non-polymer | 92.1 | 4 | Chemie (GOL) |
Sequence modifications
E, O, A, K: 199 - 302 (UniProt: P20871)
E, O, A, K: 320 - 492 (UniProt: P20871)
F, B, H, L: 1 - 183 (UniProt: P01730)
P, C, I, M: 4 - 107 (PDB: 4R2G)
P, C, I, M: 108 - 213 (UniProt: P0DOY3)
Q, D, J, N: 1 - 108 (PDB: 4R2G)
Q, D, J, N: 109 - 235 (UniProt: P0DOX5)
| PDB | External Database | Details |
|---|---|---|
| Asp 92 | - | expression tag |
| Phe 93 | - | expression tag |
| Asn 94 | - | expression tag |
| Met 95 | - | expression tag |
| Trp 96 | - | expression tag |
| Lys 97 | - | expression tag |
| Asn 98 | - | expression tag |
| Asn 99 | - | expression tag |
| Met 100 | - | expression tag |
| Val 101 | - | expression tag |
| Glu 102 | - | expression tag |
| Gln 103 | - | expression tag |
| Met 104 | - | expression tag |
| Gln 105 | - | expression tag |
| Glu 106 | - | expression tag |
| Asp 107 | - | expression tag |
| Val 108 | - | expression tag |
| Ile 109 | - | expression tag |
| Asn 110 | - | expression tag |
| Leu 111 | - | expression tag |
| Trp 112 | - | expression tag |
| Asp 113 | - | expression tag |
| Gln 114 | - | expression tag |
| Ser 115 | - | expression tag |
| Leu 116 | - | expression tag |
| Lys 117 | - | expression tag |
| Pro 118 | - | expression tag |
| Cys 119 | - | expression tag |
| Val 120 | - | expression tag |
| Lys 121 | - | expression tag |
| Leu 122 | - | expression tag |
| Thr 123 | - | expression tag |
| Gly 197 | - | expression tag |
| Gly 198 | - | expression tag |
| PDB | External Database | Details |
|---|---|---|
| Thr 317 | - | linker |
| Arg 318 | - | linker |
| Pro 319 | - | linker |
| PDB | External Database | Details |
|---|---|---|
| Met 0 | - | initiating methionine |
P, C, I, M: 108 - 213 (UniProt: P0DOY3)
Q, D, J, N: 1 - 108 (PDB: 4R2G)
Q, D, J, N: 109 - 235 (UniProt: P0DOX5)
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 16 |
| Total formula weight | 414763.6 | |
| Branched | Number of molecules | 6 |
| Total formula weight | 7734.9 | |
| Non-Polymers* | Number of molecules | 34 |
| Total formula weight | 6261.6 | |
| All* | Total formula weight | 428760.1 |
