6CDE
Cryo-EM structure at 3.8 A resolution of vaccine-elicited antibody vFP20.01 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, I, W (h, H, 3) | vFP20.01 Heavy Chain | polymer | 211 | 22673.6 | 3 | Homo sapiens (human) | ||
| 2 | B, J, X (l, L, 4) | vFP20.01 Light chain | polymer | 216 | 23826.7 | 3 | Homo sapiens (human) | ||
| 3 | C, K, Q (M, m, 7) | PGT122 Heavy chain | polymer | 228 | 24710.8 | 3 | Homo sapiens (human) | ||
| 4 | D, L, R (N, n, 8) | PGT122 Light Chain | polymer | 210 | 22560.9 | 3 | Homo sapiens (human) | ||
| 5 | E, M, S (R, r, 6) | VRC03 Light Chain | polymer | 208 | 23043.7 | 3 | Homo sapiens (human) | ||
| 6 | F, N, T (Q, q, 5) | VRC03 Heavy Chain | polymer | 227 | 24653.8 | 3 | Homo sapiens (human) | ||
| 7 | G, O, U (D, d, 1) | Glycoprotein 41 | polymer | 153 | 17162.5 | 3 | UniProt (Q2N0S7) Pfam (PF00517) | Human immunodeficiency virus 1 | |
| 8 | H, P, V (C, c, 2) | Glycoprotein 120 | polymer | 473 | 52987.0 | 3 | UniProt (Q2N0S5) Pfam (PF00516) | Human immunodeficiency virus 1 | |
| 9 | AB, CB, EB, FB, GB... (s, u, w, x, y...) | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 586.5 | 18 | In PDB GlyTouCan (G15407YE) | |||
| 10 | AA, BA, FA, IA, IB... (E, F, K, S, 0...) | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 424.4 | 12 | In PDB GlyTouCan (G42666HT) | |||
| 11 | CA, KB, TA (G, AA, f) | 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) | |||
| 12 | DA, LB, UA (I, BA, g) | 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) | |||
| 13 | EA, MB, VA (J, CA, i) | 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)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 1397.2 | 3 | In PDB GlyTouCan (G83582BK) | |||
| 14 | GA, OB, XA (O, EA, k) | 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 | 3 | In PDB GlyTouCan (G22768VO) | |||
| 15 | HA, PB, YA (P, FA, o) | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-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 | 1397.2 | 3 | In PDB GlyTouCan (G33303XH) | |||
| 16 | BB, KA, SB (t, U, IA) | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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 | 1559.4 | 3 | In PDB GlyTouCan (G63337SS) | |||
| 17 | DB, MA, UB (v, W, KA) | 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) | |||
| 18 | AC, BC, DC, EC, FC... (C, d, c, 1, 2...) | 2-acetamido-2-deoxy-beta-D-glucopyranose | non-polymer | 221.2 | 9 | Chemie (NAG) | |||
| 19 | CC, GC, YB (c, 2, C) | alpha-D-mannopyranose | non-polymer | 180.2 | 3 | Chemie (MAN) |
Sequence modifications
D, d, 1: 512 - 664 (UniProt: Q2N0S7)
C, c, 2: 31 - 505 (UniProt: Q2N0S5)
| PDB | External Database | Details |
|---|---|---|
| Cys 605 | Thr 602 | conflict |
| PDB | External Database | Details |
|---|---|---|
| Cys 201 | Ile 200 | conflict |
| Asn 332 | Thr 330 | conflict |
| Cys 433 | Ala 430 | conflict |
| Cys 501 | Ala 498 | conflict |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 24 |
| Total formula weight | 634856.9 | |
| Branched | Number of molecules | 51 |
| Total formula weight | 39155.6 | |
| Non-Polymers* | Number of molecules | 12 |
| Total formula weight | 2531.3 | |
| All* | Total formula weight | 676543.9 |
