6YHG

Thrombin in complex with D-Phe-Pro-m-methoxybenzylamide derivative (16a)

PDB DOI: https://doi.org/10.2210/pdb6YHG/pdb

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

Deposited: 2020-03-29 Released: 2021-04-07
Deposition Author(s): Sandner, A., Heine, A., Klebe, G., Collins, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.33 Å
R-Value Free: 0.145
R-Value Work: 0.123
R-Value Observed: 0.124

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 D-Phe-Pro-m-methoxybenzylamide derivative (16a)

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

To be published.

Macromolecule Content

Total Structure Weight: 36.3 kDa
Atom Count: 2,936
Modelled Residue Count: 294
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 [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 Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain G [auth H] MOL2 format, chain G [auth H] mmCIF format, chain G [auth H]	G [auth H]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain G [auth H] Interactions & Density Focus chain G [auth H]
DPN Query on DPN 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]	D-PHENYLALANINE C₉ H₁₁ N O₂ COLNVLDHVKWLRT-MRVPVSSYSA-N		Interactions Focus chain I [auth H] Interactions & Density Focus chain I [auth H]
SZ4 Query on SZ4 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]	1-(3-methoxyphenyl)methanamine C₈ H₁₁ N O GRRIMVWABNHKBX-UHFFFAOYSA-N		Interactions Focus chain K [auth H] Interactions & Density Focus chain K [auth H]
PRO Query on PRO Download Ideal Coordinates CCD File SDF format, chain J [auth H] MOL2 format, chain J [auth H] mmCIF format, chain J [auth H]	J [auth H]	PROLINE C₅ H₉ N O₂ ONIBWKKTOPOVIA-BYPYZUCNSA-N		Interactions Focus chain J [auth H] Interactions & Density Focus chain J [auth H]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain D [auth H] MOL2 format, chain D [auth H] mmCIF format, chain D [auth H]	D [auth H]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain D [auth H] Interactions & Density Focus chain D [auth H]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain H MOL2 format, chain H mmCIF format, chain H	H	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H Interactions & Density Focus chain H
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain E [auth H] SDF format, chain F [auth H] MOL2 format, chain E [auth H] MOL2 format, chain F [auth H] mmCIF format, chain E [auth H] mmCIF format, chain F [auth H]	E [auth H], F [auth H]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth H] Focus chain F [auth H] Interactions & Density Focus chain E [auth H] Focus chain F [auth H]