6LGM

Crystal structure of an oxido-reductase with mutation and inhibitor

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000226	biological_process	microtubule cytoskeleton organization
A	0002376	biological_process	immune system process
A	0004365	molecular_function	glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity
A	0005515	molecular_function	protein binding
A	0005634	cellular_component	nucleus
A	0005737	cellular_component	cytoplasm
A	0005739	cellular_component	mitochondrion
A	0005829	cellular_component	cytosol
A	0005856	cellular_component	cytoskeleton
A	0005886	cellular_component	plasma membrane
A	0006006	biological_process	glucose metabolic process
A	0006094	biological_process	gluconeogenesis
A	0006096	biological_process	glycolytic process
A	0006417	biological_process	regulation of translation
A	0006915	biological_process	apoptotic process
A	0008017	molecular_function	microtubule binding
A	0015630	cellular_component	microtubule cytoskeleton
A	0016491	molecular_function	oxidoreductase activity
A	0016620	molecular_function	oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
A	0016740	molecular_function	transferase activity
A	0017148	biological_process	negative regulation of translation
A	0019899	molecular_function	enzyme binding
A	0031906	cellular_component	late endosome lumen
A	0032481	biological_process	positive regulation of type I interferon production
A	0035605	molecular_function	peptidyl-cysteine S-nitrosylase activity
A	0035606	biological_process	peptidyl-cysteine S-trans-nitrosylation
A	0043123	biological_process	positive regulation of canonical NF-kappaB signal transduction
A	0043209	cellular_component	myelin sheath
A	0045087	biological_process	innate immune response
A	0046166	biological_process	glyceraldehyde-3-phosphate biosynthetic process
A	0050661	molecular_function	NADP binding
A	0050821	biological_process	protein stabilization
A	0051287	molecular_function	NAD binding
A	0051402	biological_process	neuron apoptotic process
A	0061621	biological_process	canonical glycolysis
A	0097452	cellular_component	GAIT complex
B	0000226	biological_process	microtubule cytoskeleton organization
B	0002376	biological_process	immune system process
B	0004365	molecular_function	glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity
B	0005515	molecular_function	protein binding
B	0005634	cellular_component	nucleus
B	0005737	cellular_component	cytoplasm
B	0005739	cellular_component	mitochondrion
B	0005829	cellular_component	cytosol
B	0005856	cellular_component	cytoskeleton
B	0005886	cellular_component	plasma membrane
B	0006006	biological_process	glucose metabolic process
B	0006094	biological_process	gluconeogenesis
B	0006096	biological_process	glycolytic process
B	0006417	biological_process	regulation of translation
B	0006915	biological_process	apoptotic process
B	0008017	molecular_function	microtubule binding
B	0015630	cellular_component	microtubule cytoskeleton
B	0016491	molecular_function	oxidoreductase activity
B	0016620	molecular_function	oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
B	0016740	molecular_function	transferase activity
B	0017148	biological_process	negative regulation of translation
B	0019899	molecular_function	enzyme binding
B	0031906	cellular_component	late endosome lumen
B	0032481	biological_process	positive regulation of type I interferon production
B	0035605	molecular_function	peptidyl-cysteine S-nitrosylase activity
B	0035606	biological_process	peptidyl-cysteine S-trans-nitrosylation
B	0043123	biological_process	positive regulation of canonical NF-kappaB signal transduction
B	0043209	cellular_component	myelin sheath
B	0045087	biological_process	innate immune response
B	0046166	biological_process	glyceraldehyde-3-phosphate biosynthetic process
B	0050661	molecular_function	NADP binding
B	0050821	biological_process	protein stabilization
B	0051287	molecular_function	NAD binding
B	0051402	biological_process	neuron apoptotic process
B	0061621	biological_process	canonical glycolysis
B	0097452	cellular_component	GAIT complex
C	0000226	biological_process	microtubule cytoskeleton organization
C	0002376	biological_process	immune system process
C	0004365	molecular_function	glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity
C	0005515	molecular_function	protein binding
C	0005634	cellular_component	nucleus
C	0005737	cellular_component	cytoplasm
C	0005739	cellular_component	mitochondrion
C	0005829	cellular_component	cytosol
C	0005856	cellular_component	cytoskeleton
C	0005886	cellular_component	plasma membrane
C	0006006	biological_process	glucose metabolic process
C	0006094	biological_process	gluconeogenesis
C	0006096	biological_process	glycolytic process
C	0006417	biological_process	regulation of translation
C	0006915	biological_process	apoptotic process
C	0008017	molecular_function	microtubule binding
C	0015630	cellular_component	microtubule cytoskeleton
C	0016491	molecular_function	oxidoreductase activity
C	0016620	molecular_function	oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
C	0016740	molecular_function	transferase activity
C	0017148	biological_process	negative regulation of translation
C	0019899	molecular_function	enzyme binding
C	0031906	cellular_component	late endosome lumen
C	0032481	biological_process	positive regulation of type I interferon production
C	0035605	molecular_function	peptidyl-cysteine S-nitrosylase activity
C	0035606	biological_process	peptidyl-cysteine S-trans-nitrosylation
C	0043123	biological_process	positive regulation of canonical NF-kappaB signal transduction
C	0043209	cellular_component	myelin sheath
C	0045087	biological_process	innate immune response
C	0046166	biological_process	glyceraldehyde-3-phosphate biosynthetic process
C	0050661	molecular_function	NADP binding
C	0050821	biological_process	protein stabilization
C	0051287	molecular_function	NAD binding
C	0051402	biological_process	neuron apoptotic process
C	0061621	biological_process	canonical glycolysis
C	0097452	cellular_component	GAIT complex
D	0000226	biological_process	microtubule cytoskeleton organization
D	0002376	biological_process	immune system process
D	0004365	molecular_function	glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity
D	0005515	molecular_function	protein binding
D	0005634	cellular_component	nucleus
D	0005737	cellular_component	cytoplasm
D	0005739	cellular_component	mitochondrion
D	0005829	cellular_component	cytosol
D	0005856	cellular_component	cytoskeleton
D	0005886	cellular_component	plasma membrane
D	0006006	biological_process	glucose metabolic process
D	0006094	biological_process	gluconeogenesis
D	0006096	biological_process	glycolytic process
D	0006417	biological_process	regulation of translation
D	0006915	biological_process	apoptotic process
D	0008017	molecular_function	microtubule binding
D	0015630	cellular_component	microtubule cytoskeleton
D	0016491	molecular_function	oxidoreductase activity
D	0016620	molecular_function	oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
D	0016740	molecular_function	transferase activity
D	0017148	biological_process	negative regulation of translation
D	0019899	molecular_function	enzyme binding
D	0031906	cellular_component	late endosome lumen
D	0032481	biological_process	positive regulation of type I interferon production
D	0035605	molecular_function	peptidyl-cysteine S-nitrosylase activity
D	0035606	biological_process	peptidyl-cysteine S-trans-nitrosylation
D	0043123	biological_process	positive regulation of canonical NF-kappaB signal transduction
D	0043209	cellular_component	myelin sheath
D	0045087	biological_process	innate immune response
D	0046166	biological_process	glyceraldehyde-3-phosphate biosynthetic process
D	0050661	molecular_function	NADP binding
D	0050821	biological_process	protein stabilization
D	0051287	molecular_function	NAD binding
D	0051402	biological_process	neuron apoptotic process
D	0061621	biological_process	canonical glycolysis
D	0097452	cellular_component	GAIT complex

Functional Information from PDB Data

site_id	AC1
Number of Residues	30
Details	binding site for residue NAD A 401

Chain	Residue
A	ASN9
A	ARG80
A	SER98
A	THR99
A	GLY100
A	PHE102
A	SER122
A	ALA123
A	ALA183
A	ASN316
A	TYR320
A	GLY10
A	PO4402
A	9HB403
A	HOH514
A	HOH519
A	HOH522
A	HOH523
A	HOH534
A	HOH537
A	HOH576
A	HOH594
A	GLY12
C	PRO191
A	ARG13
A	ILE14
A	ASN34
A	ASP35
A	PRO36
A	PHE37

---

site_id	AC2
Number of Residues	5
Details	binding site for residue PO4 A 402

Chain	Residue
A	THR182
A	THR184
A	ARG234
A	NAD401
A	HOH531

---

site_id	AC3
Number of Residues	9
Details	binding site for residue 9HB A 403

Chain	Residue
A	PRO124
A	SER151
A	SER152
A	THR153
A	THR211
A	GLY212
A	ALA213
A	NAD401
A	HOH537

---

site_id	AC4
Number of Residues	26
Details	binding site for residue NAD B 401

Chain	Residue
B	ASN9
B	GLY10
B	PHE11
B	GLY12
B	ARG13
B	ILE14
B	ASN34
B	ASP35
B	PRO36
B	PHE37
B	ARG80
B	SER98
B	THR99
B	GLY100
B	PHE102
B	SER122
B	ALA123
B	SER152
B	ALA183
B	ASN316
B	TYR320
B	PO4402
B	9HB403
B	HOH528
B	HOH564
D	PRO191

---

site_id	AC5
Number of Residues	5
Details	binding site for residue PO4 B 402

Chain	Residue
B	THR182
B	ARG234
B	NAD401
B	9HB403
B	HOH501

---

site_id	AC6
Number of Residues	9
Details	binding site for residue 9HB B 403

Chain	Residue
B	SER151
B	SER152
B	THR153
B	HIS179
B	THR211
B	GLY212
B	ALA213
B	NAD401
B	PO4402

---

site_id	AC7
Number of Residues	27
Details	binding site for residue NAD C 401

Chain	Residue
C	SER122
C	ALA123
C	ALA183
C	ASN316
C	TYR320
C	PO4402
C	9HB403
C	HOH526
C	HOH541
C	HOH544
C	HOH559
C	HOH560
A	PRO191
C	ASN9
C	GLY10
C	GLY12
C	ARG13
C	ILE14
C	ASN34
C	ASP35
C	PRO36
C	PHE37
C	ARG80
C	SER98
C	THR99
C	GLY100
C	PHE102

---

site_id	AC8
Number of Residues	5
Details	binding site for residue PO4 C 402

Chain	Residue
C	THR182
C	THR184
C	ARG234
C	NAD401
C	9HB403

---

site_id	AC9
Number of Residues	9
Details	binding site for residue 9HB C 403

Chain	Residue
C	SER151
C	SER152
C	THR153
C	HIS179
C	THR211
C	GLY212
C	ALA213
C	NAD401
C	PO4402

---

site_id	AD1
Number of Residues	6
Details	binding site for residue PO4 D 401

Chain	Residue
D	SER151
D	THR211
D	GLY212
D	ALA213
D	HOH510
D	HOH573

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	580
Details	Region: {"description":"Interaction with WARS1","evidences":[{"source":"UniProtKB","id":"P04406","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
Number of Residues	20
Details	Motif: {"description":"[IL]-x-C-x-x-[DE] motif","evidences":[{"source":"UniProtKB","id":"P04406","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI3
Number of Residues	4
Details	Active site: {"description":"Nucleophile","evidences":[{"source":"PROSITE-ProRule","id":"PRU10009","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI4
Number of Residues	20
Details	Binding site: {"evidences":[{"source":"UniProtKB","id":"P04406","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI5
Number of Residues	20
Details	Binding site: {"evidences":[{"source":"UniProtKB","id":"P22513","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI6
Number of Residues	4
Details	Site: {"description":"Activates thiol group during catalysis","evidences":[{"source":"UniProtKB","id":"P04406","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI7
Number of Residues	20
Details	Modified residue: {"description":"N6,N6-dimethyllysine","evidences":[{"source":"UniProtKB","id":"P04406","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI8
Number of Residues	28
Details	Modified residue: {"description":"Deamidated asparagine","evidences":[{"source":"UniProtKB","id":"P04406","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI9
Number of Residues	4
Details	Modified residue: {"description":"Phosphotyrosine","evidences":[{"source":"UniProtKB","id":"P04406","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI10
Number of Residues	12
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"UniProtKB","id":"P04406","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI11
Number of Residues	32
Details	Modified residue: {"description":"Phosphothreonine","evidences":[{"source":"UniProtKB","id":"P04406","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI12
Number of Residues	24
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"UniProtKB","id":"P04406","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI13
Number of Residues	4
Details	Modified residue: {"description":"S-nitrosocysteine; in reversibly inhibited form","evidences":[{"source":"UniProtKB","id":"P04797","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI14
Number of Residues	8
Details	Modified residue: {"description":"N6-malonyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P04406","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI15
Number of Residues	4
Details	Modified residue: {"description":"N6-acetyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P04406","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI16
Number of Residues	4
Details	Modified residue: {"description":"S-nitrosocysteine","evidences":[{"source":"UniProtKB","id":"P04406","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI17
Number of Residues	8
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)","evidences":[{"source":"UniProtKB","id":"P04406","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---