aTYR PHARMA INC 10-Q

Item 5. Other Information None. 60 Item 6. Exhibits Index to Exhibits Incorporated by Reference Exhibit Number Exhibit Title Form File No. Exhibit Filing Date 3.1 Restated Certificate of Incorporation of the Registrant 10-Q 001-37378 3.1 November 14, 2022 3.2 Certificate of Amendment to Restated Certificate of Incorporation of the Registrant 8-K 001-37378 3.1 June 28, 2019 3.3 Certificate of Amendment to Restated Certificate of Incorporation of the Registrant 10-Q 001-37378 3.3 May 12, 2020 3.4 Certificate of Amendment to Restated Certificate of Incorporation of the Registrant 8-K 001-37378 3.1 May 4, 2021 3.5 Certificate of Amendment to Restated Certificate of Incorporation of the Registrant 8-K 001-37378 3.1 April 29, 2022 3.6 Certificate of Amendment to Restated Certificate of Incorporation of the Registrant 8-K 001-37378 3.1 May 19, 2023 3.7 Amended and Restated Bylaws of the Registrant 10-Q 333-203272 3.6 November 14, 2022 4.1 Specimen Common Stock Certificate S-1/A 333-203272 4.1 April 27, 2015 4.2 Warrant to Purchase Stock issued to Silicon Valley Bank on December 22, 2017 10-K 001-37378 4.8 March 20, 2018 4.3 Warrant to Purchase Stock issued to Solar Capital Ltd. on December 22, 2017 10-K 001-37378 4.9 March 20, 2018 10.1 aTyr Pharma, Inc. 2015 Stock Option and Incentive Plan, as amended 8-K 001-37378 10.1 May 29, 2024 31.1 Certification of Principal Executive Officer required by Rule 13a-14(a) or Rule 15d-14(a) of the Securities Exchange Act of 1934, as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002 — — — Filed herewith 31.2 Certification of Principal Financial Officer required by Rule 13a-14(a) or Rule 15d-14(a) of the Securities Exchange Act of 1934, as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002 — — — Filed herewith 32.1# Certification of Principal Executive Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002 — — — Furnished herewith 32.2# Certification of Principal Financial Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002 — — — Furnished herewith 101.INS Inline XBRL Instance Document – the instance document does not appear in the Interactive Data File because XBRL tags are embedded within the Inline XBRL document — — — Filed herewith 101.SCH Inline XBRL Taxonomy Extension Schema With Embedded Linkbase Document — — — Filed herewith 61 Incorporated by Reference Exhibit Number Exhibit Title Form File No. Exhibit Filing Date 104 Cover Page Interactive Data File (embedded within the Inline XBRL document) — — — Filed herewith # The information in Exhibits 32.1 and 32.2 shall not be deemed “filed” for purposes of Section 18 of the Exchange Act, or otherwise subject to the liabilities of that section, nor shall it be deemed incorporated by reference in any filing under the Securities Act or the Exchange Act (including this Quarterly Report), unless the Registrant specifically incorporates the foregoing information into those documents by reference. 62 SIGNAT URES Pursuant to the requirements of the Securities Exchange Act of 1934, the registrant has duly caused this report to be signed on its behalf by the undersigned thereunto duly authorized. aTyr Pharma, Inc. Date: August 13, 2024 By: /s/ Sanjay S. Shukla Sanjay S. Shukla, M.D., M.S. President, Chief Executive Officer and Director (Principal Executive Officer) By: /s/ Jill M. Broadfoot Jill M. Broadfoot Chief Financial Officer (Principal Financial and Accounting Officer) 63