9NND
Structure of the HERV-K (HML-2) spike complex
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | A, C, D (a, c, b) | Endogenous retrovirus group K member 7 Pol protein | polymer | 248 | 27730.8 | 3 | UniProt (P63135) Pfam (PF00517) | Homo sapiens (human) | HERV-K(III) Pol protein,HERV-K102 Pol protein,HERV-K_1q22 provirus ancestral Pol protein |
| 2 | B, E, F (A, B, C) | Surface protein | polymer | 376 | 42729.1 | 3 | UniProt (P61570) Pfam (PF13804) | Homo sapiens (human) | SU |
| 3 | AA, G, H, K, L... (X, D, E, H, I...) | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 424.4 | 15 | In PDB GlyTouCan (G42666HT) | |||
| 4 | I, P, S (F, M, P) | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 570.5 | 3 | In PDB GlyTouCan (G21290RB) | |||
| 5 | J, T, X (G, Q, U) | 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) | |||
| 6 | BA, CA, DA, EA, FA... (a, A, c, b, B...) | 2-acetamido-2-deoxy-beta-D-glucopyranose | non-polymer | 221.2 | 6 | Chemie (NAG) | |||
| 7 | HA, IA, JA, KA, LA... (a, A, c, b, B...) | water | water | 18.0 | 1626 | Chemie (HOH) |
Sequence modifications
a, c, b: 466 - 699 (UniProt: P63135)
A, B, C: 90 - 465 (UniProt: P61570)
| PDB | External Database | Details |
|---|---|---|
| Gly 700 | - | expression tag |
| Ser 701 | - | expression tag |
| Gly 702 | - | expression tag |
| Gly 703 | - | expression tag |
| Gly 704 | - | expression tag |
| Gly 705 | - | expression tag |
| Asp 706 | - | expression tag |
| Tyr 707 | - | expression tag |
| Lys 708 | - | expression tag |
| Asp 709 | - | expression tag |
| Asp 710 | - | expression tag |
| Asp 711 | - | expression tag |
| Asp 712 | - | expression tag |
| Lys 713 | - | expression tag |
| PDB | External Database | Details |
|---|---|---|
| Arg 167 | Thr 167 | conflict |
| Thr 185 | Ile 185 | conflict |
| Ile 328 | Val 328 | conflict |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 6 |
| Total formula weight | 211379.6 | |
| Branched | Number of molecules | 21 |
| Total formula weight | 10810.1 | |
| Non-Polymers* | Number of molecules | 6 |
| Total formula weight | 1327.2 | |
| All* | Total formula weight | 223516.9 |
