8FK5
Cryo-EM Structure of PG9RSH DU011 Fab in complex with BG505 DS-SOSIP.664
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, F | Envelope glycoprotein gp41 | polymer | 153 | 17146.5 | 3 | UniProt (Q2N0S6) Pfam (PF00517) In PDB | Human immunodeficiency virus 1 | Env polyprotein |
| 2 | C, G, I | Envelope glycoprotein gp120 | polymer | 481 | 54086.3 | 3 | UniProt (Q2N0S6) Pfam (PF00516) In PDB | Human immunodeficiency virus 1 | Env polyprotein |
| 3 | H | Immunoblobulin G1 Fab heavy chain variable region (Fragment) | polymer | 248 | 27260.3 | 1 | UniProt (A4F255) Pfam (PF07686) Pfam (PF07654) In PDB | Homo sapiens (human) | |
| 4 | L | Immunoglobulin lambda-1 light chain-like | polymer | 216 | 22804.2 | 1 | UniProt (Q6PJG0) Pfam (PF07686) Pfam (PF07654) In PDB | Homo sapiens (human) | |
| 5 | b, c, D, E, K... | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 424.4 | 16 | In PDB GlyTouCan (G42666HT) | |||
| 6 | J, Q, X | 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) | |||
| 7 | a, d, V | 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) | |||
| 8 | e | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[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 | 1559.4 | 1 | In PDB GlyTouCan (G83161QT) | |||
| 9 | G, A, B, I, C... | 2-acetamido-2-deoxy-beta-D-glucopyranose | non-polymer | 221.2 | 38 | Chemie (NAG) |
Sequence modifications
A, B, F: 512 - 664 (UniProt: Q2N0S6)
C, G, I: 31 - 513 (UniProt: Q2N0S6)
H: 4 - 218 (UniProt: A4F255)
L: 1 - 212 (UniProt: Q6PJG0)
| PDB | External Database | Details |
|---|---|---|
| Pro 559 | Ile 556 | conflict |
| 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 |
| Arg 509 | Glu 506 | conflict |
| Arg 510 | Lys 507 | conflict |
| Arg 512 | Ala 509 | conflict |
| Arg 513 | Val 510 | conflict |
| PDB | External Database | Details |
|---|---|---|
| Glu 2 | - | expression tag |
| Arg 3 | - | expression tag |
| Val 5 | Glu 2 | conflict |
| Ser 16 | Lys 13 | conflict |
| Ala 23 | Thr 20 | conflict |
| Asp 28 | Ile 25 | conflict |
| Arg 31 | Asp 28 | conflict |
| Gln 32 | Phe 29 | conflict |
| Gln 43 | Lys 40 | conflict |
| Trp 47 | Ser 44 | conflict |
| Phe 50 | Thr 47 | conflict |
| Lys 52 | Trp 49 | conflict |
| Tyr 52 | Ser 50 | conflict |
| Glu 56 | Asn 54 | conflict |
| Lys 57 | Glu 55 | conflict |
| Tyr 58 | Lys 56 | conflict |
| His 59 | Tyr 57 | conflict |
| Trp 64 | Thr 62 | conflict |
| Leu 67 | Phe 65 | conflict |
| Ser 68 | Ala 66 | conflict |
| Asp 76 | Asn 74 | conflict |
| Thr 77 | Met 75 | conflict |
| Gln 81 | His 79 | conflict |
| Asn 82 | Asp 81 | conflict |
| Ser 82 | Asn 82 | conflict |
| Val 84 | Ala 85 | conflict |
| Thr 89 | Val 90 | conflict |
| Phe 91 | Tyr 92 | conflict |
| Val 93 | Ala 94 | conflict |
| Glu 95 | Asp 96 | conflict |
| Gly 97 | - | insertion |
| Gly 98 | - | insertion |
| Pro 99 | - | insertion |
| Tyr 100 | Met 99 | conflict |
| Arg 100 | Ile 100 | conflict |
| Asn 100 | Thr 101 | conflict |
| Gly 100 | Phe 102 | conflict |
| Tyr 100 | Ala 103 | conflict |
| Tyr 100 | Arg 104 | conflict |
| Tys 100 | Ile 105 | conflict |
| Tys 100 | Leu 106 | conflict |
| - | Pro 108 | deletion |
| - | Pro 109 | deletion |
| Tyr 100 | His 111 | conflict |
| Asp 100 | Lys 112 | conflict |
| Tyr 100 | - | insertion |
| Tyr 100 | - | insertion |
| Asn 100 | - | insertion |
| Tyr 100 | - | insertion |
| His 100 | - | insertion |
| Tyr 100 | - | insertion |
| Lys 105 | Gln 119 | conflict |
| Thr 110 | Ile 124 | conflict |
| Gly 219 | - | expression tag |
| Leu 220 | - | expression tag |
| Glu 221 | - | expression tag |
| Val 222 | - | expression tag |
| Leu 223 | - | expression tag |
| Phe 224 | - | expression tag |
| Gln 225 | - | expression tag |
| PDB | External Database | Details |
|---|---|---|
| Gln 24 | Thr 42 | conflict |
| Asn 27 | Thr 46 | conflict |
| Gly 29 | Ser 50 | conflict |
| Tyr 30 | His 51 | conflict |
| Glu 31 | Ser 52 | conflict |
| Ser 32 | Leu 53 | conflict |
| Val 46 | Phe 67 | conflict |
| Val 47 | Leu 68 | conflict |
| Tyr 49 | Phe 70 | conflict |
| Asp 50 | Glu 71 | conflict |
| Val 51 | Gly 72 | conflict |
| Gly 84 | Ala 105 | conflict |
| Lys 89 | Cys 110 | conflict |
| Leu 91 | Tyr 112 | conflict |
| Thr 92 | Val 113 | conflict |
| Ser 93 | Gly 114 | conflict |
| Arg 94 | Ser 115 | conflict |
| Ser 95 | Gly 116 | conflict |
| His 95 | Thr 117 | conflict |
| Arg 96 | Val 118 | conflict |
| Thr 100 | Gly 122 | conflict |
| Lys 189 | Arg 212 | conflict |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 8 |
| Total formula weight | 263762.9 | |
| Branched | Number of molecules | 23 |
| Total formula weight | 14301.2 | |
| Non-Polymers* | Number of molecules | 38 |
| Total formula weight | 8405.9 | |
| All* | Total formula weight | 286469.9 |
