2GD4
Crystal Structure of the Antithrombin-S195A Factor Xa-Pentasaccharide Complex
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | A, D (L, A) | Coagulation factor X, Stuart factor, Stuart-Prower factor, Contains: Factor X light chain; Factor X heavy chain; Activated factor Xa heavy chain | polymer | 58 | 6478.4 | 2 | UniProt (P00742) Pfam (PF14670) | Homo sapiens (human) | |
| 2 | B, E (H, B) | Coagulation factor, Stuart factor, Stuart-Prower factor, Contains: Factor X light chain; Factor X heavy chain; Activated factor Xa heavy chain | polymer | 241 | 27185.1 | 2 | UniProt (P00742) Pfam (PF00089) | Homo sapiens (human) | |
| 3 | C, F (I, C) | Antithrombin-III | polymer | 443 | 50162.3 | 2 | UniProt (P01008) Pfam (PF00079) | Homo sapiens (human) | ATIII |
| 4 | G (D) | 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 | 1 | In PDB GlyTouCan (G56014GC) | |||
| 5 | H (E) | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 424.4 | 1 | In PDB GlyTouCan (G42666HT) | |||
| 6 | I, J (F, G) | 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-4)-2-deoxy-3,6-di-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-methyl 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranoside | branched | 1508.3 | 2 | In PDB BIRD (PRD_900028) GlyTouCan (G25282IW) | fondaparinux | ||
| 7 | K, N (H, B) | CALCIUM ION | non-polymer | 40.1 | 2 | Chemie (CA) | |||
| 8 | L, M, O, P (I, C) | 2-acetamido-2-deoxy-beta-D-glucopyranose | non-polymer | 221.2 | 4 | Chemie (NAG) | |||
| 9 | Q, R, S, T, U... (L, H, I, A, B...) | water | water | 18.0 | 63 | Chemie (HOH) |
Sequence modifications
L, A: 86 - 142 (UniProt: P00742)
H, B: 16 - 251 (UniProt: P00742)
I, C: -10 - 432 (UniProt: P01008)
| PDB | External Database | Details |
|---|---|---|
| Met 85 | - | cloning artifact |
| PDB | External Database | Details |
|---|---|---|
| Ala 104 | Ser 419 | engineered mutation |
| PDB | External Database | Details |
|---|---|---|
| Ala 137 | Ser 169 | engineered mutation |
| Ala 347 | Glu 379 | engineered mutation |
| Ala 348 | Lys 380 | engineered mutation |
| Ala 350 | Lys 382 | engineered mutation |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 6 |
| Total formula weight | 167651.5 | |
| Branched | Number of molecules | 4 |
| Total formula weight | 4513.9 | |
| Non-Polymers* | Number of molecules | 6 |
| Total formula weight | 965.0 | |
| All* | Total formula weight | 173130.4 |
