5VN3
Cryo-EM model of B41 SOSIP.664 in complex with soluble CD4 (D1-D2) and fragment antigen binding variable domain of 17b
Entity
Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
1 | L, N, O | 17b Fab light chain | polymer | 214 | 23425.9 | 3 | Homo sapiens (Human) | ||
2 | A, B, D | Envelope glycoprotein gp160 | polymer | 153 | 17357.8 | 3 | UniProt (B3UEZ6) Pfam (PF00517) In PDB | Human immunodeficiency virus 1 | |
3 | G, I, J | Envelope glycoprotein gp160 | polymer | 516 | 57702.5 | 3 | UniProt (B3UES2) Pfam (PF00516) In PDB | Human immunodeficiency virus 1 | |
4 | C, E, F | T-cell surface glycoprotein CD4 | polymer | 185 | 20503.3 | 3 | UniProt (P01730) Pfam (PF00047) Pfam (PF05790) In PDB | Homo sapiens (Human) | T-cell surface antigen T4/Leu-3 |
5 | H, K, M | 17b Fab heavy chain | polymer | 229 | 24484.5 | 3 | Homo sapiens | ||
6 | a, e, f, j, l... | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 424.4 | 12 | In PDB GlyTouCan (G42666HT) | |||
7 | b, h, i, k, m... | 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) | |||
8 | c, n, R | alpha-D-mannopyranose-(1-2)-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 | 1235.1 | 3 | In PDB GlyTouCan (G46836GH) | |||
9 | d, o, S | 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) | |||
10 | g, r, V | 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) | |||
11 | G, B, I, D, J... | 2-acetamido-2-deoxy-beta-D-glucopyranose | non-polymer | 221.2 | 24 | Chemie (NAG) |
Sequence modifications
A, B, D: 512 - 664 (UniProt: B3UEZ6)
G, I, J: 31 - 505 (UniProt: B3UES2)
C, E, F: 1 - 183 (UniProt: P01730)
PDB | External Database | Details |
---|---|---|
Pro 559 | Ile 563 | engineered mutation |
Cys 605 | Thr 609 | engineered mutation |
PDB | External Database | Details |
---|---|---|
Met -4 | - | initiating methionine |
Asp -3 | - | expression tag |
Ala -2 | - | expression tag |
Met -1 | - | expression tag |
Lys 0 | - | expression tag |
Arg 1 | - | expression tag |
Gly 2 | - | expression tag |
Leu 3 | - | expression tag |
Cys 4 | - | expression tag |
Cys 5 | - | expression tag |
Val 6 | - | expression tag |
Leu 7 | - | expression tag |
Leu 8 | - | expression tag |
Leu 9 | - | expression tag |
Cys 10 | - | expression tag |
Gly 11 | - | expression tag |
Ala 12 | - | expression tag |
Val 13 | - | expression tag |
Phe 14 | - | expression tag |
Val 15 | - | expression tag |
Ser 16 | - | expression tag |
Pro 17 | - | expression tag |
Ser 18 | - | expression tag |
Gln 19 | - | expression tag |
Glu 20 | - | expression tag |
Ile 21 | - | expression tag |
His 22 | - | expression tag |
Ala 23 | - | expression tag |
Arg 24 | - | expression tag |
Phe 25 | - | expression tag |
Arg 26 | - | expression tag |
Arg 27 | - | expression tag |
Gly 28 | - | expression tag |
Ala 29 | - | expression tag |
Arg 30 | - | expression tag |
Cys 501 | Ala 505 | engineered mutation |
PDB | External Database | Details |
---|---|---|
Asn 184 | - | expression tag |
Thr 185 | - | expression tag |
Sequence viewer
Contents of the asymmetric unit
Polymers | Number of chains | 15 |
Total formula weight | 430421.6 | |
Branched | Number of molecules | 33 |
Total formula weight | 20328.7 | |
Non-Polymers* | Number of molecules | 24 |
Total formula weight | 5309.0 | |
All* | Total formula weight | 456059.3 |