9I2H
A 3.3 angstrom cryo-EM structure of an engineered high-affinity human prothrombinase complex
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 (H) | Activated factor Xa heavy chain | polymer | 254 | 28789.9 | 1 | UniProt (P00742) Pfam (PF00089) | Homo sapiens (human) | |
| 2 | B (L) | Factor X light chain | polymer | 139 | 15765.6 | 1 | UniProt (P00742) Pfam (PF00594) Pfam (PF00008) Pfam (PF14670) | Homo sapiens (human) | |
| 3 | C (A) | Coagulation factor V heavy chain | polymer | 709 | 81354.5 | 1 | UniProt (P12259) Pfam (PF07732) | Homo sapiens (human) | |
| 4 | D (B) | Coagulation factor V light chain | polymer | 651 | 75283.0 | 1 | UniProt (P12259) Pfam (PF07732) Pfam (PF00754) | Homo sapiens (human) | |
| 5 | E (X) | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 1057.0 | 1 | In PDB GlyTouCan (G82348BZ) | |||
| 6 | F (C) | 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 | 1 | In PDB GlyTouCan (G22768VO) | |||
| 7 | G (D) | alpha-D-mannopyranose-(1-6)-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 | 1235.1 | 1 | In PDB GlyTouCan (G76882CO) | |||
| 8 | H (E) | alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 367.3 | 1 | In PDB GlyTouCan (G86851RC) | |||
| 9 | I, L (H, A) | CALCIUM ION | non-polymer | 40.1 | 2 | Chemie (CA) | |||
| 10 | J (H) | SODIUM ION | non-polymer | 23.0 | 1 | Chemie (NA) | |||
| 11 | K (H) | L-alpha-glutamyl-N-{(1S)-4-{[amino(iminio)methyl]amino}-1-[(1S)-2-chloro-1-hydroxyethyl]butyl}glycinamide | non-polymer | 395.9 | 1 | BIRD (PRD_000288) Chemie (0GJ) | |||
| 12 | M (B) | COPPER (II) ION | non-polymer | 63.5 | 1 | Chemie (CU) |
Sequence modifications
H: 16 - 264 (UniProt: P00742)
L: 1 - 139 (UniProt: P00742)
| PDB | External Database | Details |
|---|---|---|
| Asn 129 | Glu 350 | engineered mutation |
| Glu 130 | Ser 351 | engineered mutation |
| Lys 132 | Thr 355 | engineered mutation |
| Asp 134 | Lys 357 | engineered mutation |
| His 166 | Asn 388 | engineered mutation |
| Met 169 | Lys 391 | engineered mutation |
| Asp 173 | Ser 395 | engineered mutation |
| Arg 175 | Ile 397 | engineered mutation |
| Arg 233 | Ala 457 | engineered mutation |
| Lys 239 | Asp 463 | engineered mutation |
| PDB | External Database | Details |
|---|---|---|
| Arg 90 | Ser 130 | engineered mutation |
| Ala 91 | Leu 131 | engineered mutation |
| Phe 92 | Asp 132 | engineered mutation |
| Lys 101 | His 141 | engineered mutation |
| Arg 102 | Glu 142 | engineered mutation |
| Val 103 | Glu 143 | engineered mutation |
| Ser 105 | Asn 145 | engineered mutation |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 4 |
| Total formula weight | 201193.0 | |
| Branched | Number of molecules | 4 |
| Total formula weight | 3570.2 | |
| Non-Polymers* | Number of molecules | 5 |
| Total formula weight | 562.6 | |
| All* | Total formula weight | 205325.8 |
