6NF2
Cryo-EM structure of vaccine-elicited antibody 0PV-c.01 in complex with HIV-1 Env BG505 DS-SOSIP and antibodies VRC03 and PGT122
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, G, Q | Envelope glycoprotein gp120 | polymer | 480 | 53929.1 | 3 | UniProt (Q2N0S6) Pfam (PF00516) In PDB | Human immunodeficiency virus 1 | |
| 2 | B, I, R | Envelope glycoprotein gp41 | polymer | 153 | 17146.5 | 3 | UniProt (Q2N0S6) Pfam (PF00517) In PDB | Human immunodeficiency virus 1 | |
| 3 | C, N, V | VRC03 Heavy Chain | polymer | 235 | 25450.6 | 3 | Homo sapiens (human) | ||
| 4 | D, M, U | VRC03 Light Chain | polymer | 209 | 23146.8 | 3 | Homo sapiens (human) | ||
| 5 | E, J, S | PGT122 Heavy Chain | polymer | 235 | 25434.7 | 3 | Homo sapiens (human) | ||
| 6 | F, K, T | PGT122 Light Chain | polymer | 213 | 22880.3 | 3 | Homo sapiens (human) | ||
| 7 | H, O, W | 0PV-c.01 Heavy Chain | polymer | 229 | 24179.2 | 3 | Homo sapiens (human) | ||
| 8 | L, P, X | 0PV-c.01 Light Chain | polymer | 219 | 23966.7 | 3 | Homo sapiens (human) | ||
| 9 | 0, 4, 5, g, h... | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 424.4 | 15 | In PDB GlyTouCan (G42666HT) | |||
| 10 | a, 3, 6, n, q... | 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 | 6 | In PDB GlyTouCan (G81315DD) | |||
| 11 | b, 7, j, FA, r... | 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 | 6 | In PDB GlyTouCan (G22768VO) | |||
| 12 | c, 2, e, i, 8... | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 586.5 | 12 | In PDB GlyTouCan (G15407YE) | |||
| 13 | d, 9, t | 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 | 748.7 | 3 | In PDB GlyTouCan (G22573RC) | |||
| 14 | f, BA, 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) | |||
| 15 | 1, l, HA | 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) | |||
| 16 | Q, R, A, B, G... | 2-acetamido-2-deoxy-beta-D-glucopyranose | non-polymer | 221.2 | 9 | Chemie (NAG) |
Sequence modifications
A, G, Q: 31 - 512 (UniProt: Q2N0S6)
B, I, R: 512 - 664 (UniProt: Q2N0S6)
| PDB | External Database | Details |
|---|---|---|
| Cys 201 | Ile 200 | engineered mutation |
| Asn 332 | Thr 330 | engineered mutation |
| Cys 433 | Ala 430 | engineered mutation |
| Cys 501 | Ala 498 | engineered mutation |
| Arg 509 | Glu 506 | engineered mutation |
| Arg 510 | Lys 507 | engineered mutation |
| Arg 512 | Ala 509 | engineered mutation |
| 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 | 24 |
| Total formula weight | 648401.6 | |
| Branched | Number of molecules | 48 |
| Total formula weight | 33504.6 | |
| Non-Polymers* | Number of molecules | 9 |
| Total formula weight | 1990.9 | |
| All* | Total formula weight | 683897.1 |
