6Y02

Thrombin in complex with 13k

PDB DOI: https://doi.org/10.2210/pdb6Y02/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens, Hirudo medicinalis
Mutation(s): No

Deposited: 2020-02-06 Released: 2021-02-17
Deposition Author(s): Sandner, A., Heine, A., Klebe, G., Abazi, N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.48 Å
R-Value Free: 0.164
R-Value Work: 0.139
R-Value Observed: 0.140

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Thrombin in complex with 13k

Sandner, A., Heine, A., Klebe, G.

To be published.

Macromolecule Content

Total Structure Weight: 36.55 kDa
Atom Count: 2,661
Modelled Residue Count: 289
Deposited Residue Count: 307
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
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 Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
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	Glycosylation Focus chain B [auth H]	Go to GlyGen: P00734-1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Hirudin variant-2	C	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 Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
O5Z (Subject of Investigation/LOI) Query on O5Z Download Ideal Coordinates CCD File SDF format, chain I [auth H] MOL2 format, chain I [auth H] mmCIF format, chain I [auth H]	I [auth H]	(2~{S})-1-[(2~{R})-2-azanyl-3-phenyl-propanoyl]-~{N}-[(5-bromanylfuran-2-yl)methyl]pyrrolidine-2-carboxamide C₁₉ H₂₂ Br N₃ O₃ BLTHEFKWZUYOME-CVEARBPZSA-N		Interactions Focus chain I [auth H] Interactions & Density Focus chain I [auth H]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain K [auth H] MOL2 format, chain K [auth H] mmCIF format, chain K [auth H]	K [auth H]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain K [auth H] Interactions & Density Focus chain K [auth H]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain F [auth H] MOL2 format, chain F [auth H] mmCIF format, chain F [auth H]	F [auth H]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain F [auth H] Interactions & Density Focus chain F [auth H]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain H SDF format, chain L [auth H] MOL2 format, chain H MOL2 format, chain L [auth H] mmCIF format, chain H mmCIF format, chain L [auth H]	H, L [auth H]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H Focus chain L [auth H] Interactions & Density Focus chain H Focus chain L [auth H]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain G [auth H] SDF format, chain J [auth H] MOL2 format, chain G [auth H] MOL2 format, chain J [auth H] mmCIF format, chain G [auth H] mmCIF format, chain J [auth H]	G [auth H], J [auth H]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain G [auth H] Focus chain J [auth H] Interactions & Density Focus chain G [auth H] Focus chain J [auth H]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain D [auth H] SDF format, chain E [auth H] MOL2 format, chain D [auth H] MOL2 format, chain E [auth H] mmCIF format, chain D [auth H] mmCIF format, chain E [auth H]	D [auth H], E [auth H]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain D [auth H] Focus chain E [auth H] Interactions & Density Focus chain D [auth H] Focus chain E [auth H]