6XCY | pdb_00006xcy

Porcine pepsin in complex with ritonavir

PDB DOI: https://doi.org/10.2210/pdb6XCY/pdb

Classification: HYDROLASE/INHIBITOR
Organism(s): Sus scrofa
Mutation(s): No

Deposited: 2020-06-09 Released: 2021-06-16
Deposition Author(s): Vuksanovic, N., Silvaggi, N.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free:
0.235 (Depositor), 0.240 (DCC)
R-Value Work:
0.191 (Depositor), 0.190 (DCC)
R-Value Observed:
0.193 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Porcine pepsin in complex with ritonavir

Vuksanovic, N., Silvaggi, N.R.

To be published.

Macromolecule Content

Total Structure Weight: 35.31 kDa
Atom Count: 2,567
Modeled Residue Count: 325
Deposited Residue Count: 326
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pepsin A	A	326	Sus scrofa	Mutation(s): 0 EC: 3.4.23.1
UniProt
Find proteins for P00791 (Sus scrofa) Explore P00791 Go to UniProtKB: P00791
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00791
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RIT (Subject of Investigation/LOI) Query on RIT Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	RITONAVIR C₃₇ H₄₈ N₆ O₅ S₂ NCDNCNXCDXHOMX-XGKFQTDJSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP Query on SEP	A	L-PEPTIDE LINKING	C₃ H₈ N O₆ P		SER

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_001001 (RIT) Query on PRD_001001	B [auth A]	RITONAVIR	Peptide-like / Inhibitor		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.235 (Depositor), 0.240 (DCC)
R-Value Work: 0.191 (Depositor), 0.190 (DCC)
R-Value Observed: 0.193 (Depositor)

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.16	α = 90
b = 66.16	β = 90
c = 285.522	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2021-06-16

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2021-06-16
Type: Initial release
Version 1.1: 2021-08-18
Changes: Data collection, Database references
Version 1.2: 2023-10-18
Changes: Data collection, Refinement description
Version 1.3: 2024-10-16
Changes: Structure summary

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.