Thrombin in complex with D-Phe-Pro-m-methoxybenzylamide derivative (16a)
Sandner, A., Heine, A., Klebe, G.To be published.
Experimental Data Snapshot
Starting Model: experimental
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Entity ID: 1 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Prothrombin | A [auth L] | 36 | Homo sapiens | Mutation(s): 0  EC: 3.4.21.5 | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P00734 (Homo sapiens) Explore P00734  Go to UniProtKB:  P00734 | |||||
PHAROS:  P00734 GTEx:  ENSG00000180210  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P00734 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 2 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Prothrombin | B [auth H] | 259 | Homo sapiens | Mutation(s): 0  EC: 3.4.21.5 | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P00734 (Homo sapiens) Explore P00734  Go to UniProtKB:  P00734 | |||||
PHAROS:  P00734 GTEx:  ENSG00000180210  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P00734 | ||||
Glycosylation | |||||
Glycosylation Sites: 1 | Go to GlyGen: P00734-1 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by: Sequence | 3D Structure
Entity ID: 3 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Hirudin variant-2 | C [auth I] | 12 | Hirudo medicinalis | Mutation(s): 0  | |
UniProt | |||||
Find proteins for P09945 (Hirudo medicinalis) Explore P09945  Go to UniProtKB:  P09945 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P09945 | ||||
Sequence AnnotationsExpand | |||||
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Ligands 7 Unique | |||||
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ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | G [auth H] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
DPN Query on DPN | I [auth H] | D-PHENYLALANINE C9 H11 N O2 COLNVLDHVKWLRT-MRVPVSSYSA-N | |||
SZ4 Query on SZ4 | K [auth H] | 1-(3-methoxyphenyl)methanamine C8 H11 N O GRRIMVWABNHKBX-UHFFFAOYSA-N | |||
PRO Query on PRO | J [auth H] | PROLINE C5 H9 N O2 ONIBWKKTOPOVIA-BYPYZUCNSA-N | |||
PO4 Query on PO4 | D [auth H] | PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K | |||
GOL Query on GOL | H | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N | |||
NA Query on NA | E [auth H], F [auth H] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |
Modified Residues 1 Unique | |||||
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ID | Chains | Type | Formula | 2D Diagram | Parent |
TYS Query on TYS | C [auth I] | L-PEPTIDE LINKING | C9 H11 N O6 S | TYR |
Length ( Å ) | Angle ( ˚ ) |
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a = 70.25 | α = 90 |
b = 71.251 | β = 100.61 |
c = 72.742 | γ = 90 |
Software Name | Purpose |
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PHENIX | refinement |
PDB_EXTRACT | data extraction |
Coot | model building |
XDS | data scaling |
XDS | data reduction |
PHASER | phasing |