Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

6I34

Crystal structure of Neanderthal glycine decarboxylase (P-protein)

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0004375	molecular_function	glycine dehydrogenase (decarboxylating) activity
A	0005654	cellular_component	nucleoplasm
A	0005739	cellular_component	mitochondrion
A	0005759	cellular_component	mitochondrial matrix
A	0005886	cellular_component	plasma membrane
A	0005960	cellular_component	glycine cleavage complex
A	0006520	biological_process	amino acid metabolic process
A	0006544	biological_process	glycine metabolic process
A	0006546	biological_process	glycine catabolic process
A	0009055	molecular_function	electron transfer activity
A	0016491	molecular_function	oxidoreductase activity
A	0016594	molecular_function	glycine binding
A	0016829	molecular_function	lyase activity
A	0019464	biological_process	glycine decarboxylation via glycine cleavage system
A	0030170	molecular_function	pyridoxal phosphate binding
A	0036255	biological_process	response to methylamine
A	0042803	molecular_function	protein homodimerization activity
A	0070280	molecular_function	pyridoxal binding
A	1903442	biological_process	response to lipoic acid
A	1990830	biological_process	cellular response to leukemia inhibitory factor
B	0004375	molecular_function	glycine dehydrogenase (decarboxylating) activity
B	0005654	cellular_component	nucleoplasm
B	0005739	cellular_component	mitochondrion
B	0005759	cellular_component	mitochondrial matrix
B	0005886	cellular_component	plasma membrane
B	0005960	cellular_component	glycine cleavage complex
B	0006520	biological_process	amino acid metabolic process
B	0006544	biological_process	glycine metabolic process
B	0006546	biological_process	glycine catabolic process
B	0009055	molecular_function	electron transfer activity
B	0016491	molecular_function	oxidoreductase activity
B	0016594	molecular_function	glycine binding
B	0016829	molecular_function	lyase activity
B	0019464	biological_process	glycine decarboxylation via glycine cleavage system
B	0030170	molecular_function	pyridoxal phosphate binding
B	0036255	biological_process	response to methylamine
B	0042803	molecular_function	protein homodimerization activity
B	0070280	molecular_function	pyridoxal binding
B	1903442	biological_process	response to lipoic acid
B	1990830	biological_process	cellular response to leukemia inhibitory factor
C	0004375	molecular_function	glycine dehydrogenase (decarboxylating) activity
C	0005654	cellular_component	nucleoplasm
C	0005739	cellular_component	mitochondrion
C	0005759	cellular_component	mitochondrial matrix
C	0005886	cellular_component	plasma membrane
C	0005960	cellular_component	glycine cleavage complex
C	0006520	biological_process	amino acid metabolic process
C	0006544	biological_process	glycine metabolic process
C	0006546	biological_process	glycine catabolic process
C	0009055	molecular_function	electron transfer activity
C	0016491	molecular_function	oxidoreductase activity
C	0016594	molecular_function	glycine binding
C	0016829	molecular_function	lyase activity
C	0019464	biological_process	glycine decarboxylation via glycine cleavage system
C	0030170	molecular_function	pyridoxal phosphate binding
C	0036255	biological_process	response to methylamine
C	0042803	molecular_function	protein homodimerization activity
C	0070280	molecular_function	pyridoxal binding
C	1903442	biological_process	response to lipoic acid
C	1990830	biological_process	cellular response to leukemia inhibitory factor
D	0004375	molecular_function	glycine dehydrogenase (decarboxylating) activity
D	0005654	cellular_component	nucleoplasm
D	0005739	cellular_component	mitochondrion
D	0005759	cellular_component	mitochondrial matrix
D	0005886	cellular_component	plasma membrane
D	0005960	cellular_component	glycine cleavage complex
D	0006520	biological_process	amino acid metabolic process
D	0006544	biological_process	glycine metabolic process
D	0006546	biological_process	glycine catabolic process
D	0009055	molecular_function	electron transfer activity
D	0016491	molecular_function	oxidoreductase activity
D	0016594	molecular_function	glycine binding
D	0016829	molecular_function	lyase activity
D	0019464	biological_process	glycine decarboxylation via glycine cleavage system
D	0030170	molecular_function	pyridoxal phosphate binding
D	0036255	biological_process	response to methylamine
D	0042803	molecular_function	protein homodimerization activity
D	0070280	molecular_function	pyridoxal binding
D	1903442	biological_process	response to lipoic acid
D	1990830	biological_process	cellular response to leukemia inhibitory factor

Functional Information from PDB Data

site_id	AC1
Number of Residues	16
Details	binding site for residue PLP A 1101

Chain	Residue
A	TYR161
A	ASP727
A	ALA729
A	ASN751
A	HIS753
A	LYS754
A	GOL1106
A	HOH1211
A	CYS382
A	THR383
A	SER557
A	GLY618
A	ALA619
A	GLU622
A	HIS651
A	THR653

site_id	AC2
Number of Residues	5
Details	binding site for residue EDO A 1102

Chain	Residue
A	HIS60
A	ARG66
A	GLU113
A	HOH1377
B	EDO1103

site_id	AC3
Number of Residues	3
Details	binding site for residue EDO A 1103

Chain	Residue
A	ARG461
A	LEU462
A	VAL785

site_id	AC4
Number of Residues	4
Details	binding site for residue EDO A 1104

Chain	Residue
A	ARG103
A	LYS106
A	GLU604
A	ARG739

site_id	AC5
Number of Residues	10
Details	binding site for residue PEG A 1105

Chain	Residue
A	ASN543
A	HIS550
A	ASN980
A	LYS981
A	PHE982
A	HOH1349
A	HOH1456
A	HOH1531
A	HOH1549
B	ASN543

site_id	AC6
Number of Residues	7
Details	binding site for residue GOL A 1106

Chain	Residue
A	TYR164
A	CYS558
A	HIS651
A	LYS754
A	THR894
A	PLP1101
A	HOH1201

site_id	AC7
Number of Residues	7
Details	binding site for residue GOL A 1107

Chain	Residue
A	ARG51
A	GLU54
A	LEU57
A	PRO58
A	ARG59
A	HOH1501
B	GLU478

site_id	AC8
Number of Residues	4
Details	binding site for residue EDO B 1102

Chain	Residue
B	HIS60
B	ARG66
B	GLU113
B	HOH1379

site_id	AC9
Number of Residues	7
Details	binding site for residue EDO B 1103

Chain	Residue
A	HIS60
A	ASP61
A	ARG66
A	EDO1102
B	HIS399
B	GLY403
B	HIS406

site_id	AD1
Number of Residues	2
Details	binding site for residue EDO B 1104

Chain	Residue
B	HIS399
B	HIS402

site_id	AD2
Number of Residues	8
Details	binding site for residue PEG B 1105

Chain	Residue
A	ASN543
A	HOH1531
B	ASN980
B	LYS981
B	PHE982
B	TRP983
B	HOH1243
B	HOH1440

site_id	AD3
Number of Residues	6
Details	binding site for residue EDO C 1102

Chain	Residue
C	ASN140
C	CYS141
C	LEU297
C	ARG319
C	ASP473
C	GLU474

site_id	AD4
Number of Residues	3
Details	binding site for residue EDO C 1103

Chain	Residue
C	ARG461
C	LEU462
C	VAL785

site_id	AD5
Number of Residues	7
Details	binding site for residue EDO C 1104

Chain	Residue
C	GLN208
C	ASP375
C	ALA377
C	SER379
C	ALA656
C	HIS659
C	MET660

site_id	AD6
Number of Residues	7
Details	binding site for residue PEG C 1105

Chain	Residue
C	ASN543
C	ASN980
C	LYS981
C	PHE982
C	HOH1452
C	HOH1483
D	ASN543

site_id	AD7
Number of Residues	10
Details	binding site for residue PEG C 1106

Chain	Residue
C	ASN114
C	HOH1246
C	HOH1324
D	SER142
D	HIS399
D	EDO1103
D	HOH1239
C	ASP61
C	ARG66
C	GLU113

site_id	AD8
Number of Residues	7
Details	binding site for residue GOL C 1107

Chain	Residue
C	ARG51
C	GLU54
C	LEU57
C	ARG59
C	HOH1284
D	GLU478
D	HOH1379

site_id	AD9
Number of Residues	9
Details	binding site for residue GOL C 1108

Chain	Residue
C	TYR164
C	GLY556
C	SER557
C	CYS558
C	HIS651
C	LYS754
C	THR894
C	PLP1101
C	HOH1201

site_id	AE1
Number of Residues	6
Details	binding site for residue PEG D 1101

Chain	Residue
C	ASN543
D	ASN543
D	LYS981
D	PHE982
D	HOH1336
D	HOH1415

site_id	AE2
Number of Residues	6
Details	binding site for residue EDO D 1103

Chain	Residue
C	HIS60
C	ASP61
C	ARG66
C	PEG1106
D	HIS399
D	GLY403

site_id	AE3
Number of Residues	4
Details	binding site for residue EDO D 1104

Chain	Residue
D	ASP61
D	ARG66
D	GLU113
D	HOH1289

site_id	AE4
Number of Residues	6
Details	binding site for residue GOL D 1105

Chain	Residue
D	TYR164
D	GLN370
D	HIS371
D	HIS651
D	LYS754
D	PLP1102

site_id	AE5
Number of Residues	20
Details	binding site for Di-peptide PLP B 1101 and LYS B 754

Chain	Residue
B	CYS382
B	THR383
B	SER557
B	CYS558
B	THR559
B	SER617
B	GLY618
B	ALA619
B	GLU622
B	HIS651
B	THR653
B	ASP727
B	ALA729
B	ASN751
B	LEU752
B	HIS753
B	THR755
B	PHE756
B	HOH1206
B	HOH1410

site_id	AE6
Number of Residues	21
Details	binding site for Di-peptide PLP C 1101 and LYS C 754

Chain	Residue
C	CYS382
C	THR383
C	SER557
C	CYS558
C	THR559
C	SER617
C	GLY618
C	ALA619
C	GLU622
C	HIS651
C	THR653
C	ASP727
C	ALA729
C	ASN751
C	LEU752
C	HIS753
C	THR755
C	PHE756
C	GOL1108
C	HOH1237
C	HOH1509

site_id	AE7
Number of Residues	21
Details	binding site for Di-peptide PLP D 1102 and LYS D 754

Chain	Residue
D	CYS382
D	THR383
D	SER557
D	CYS558
D	THR559
D	SER617
D	GLY618
D	ALA619
D	GLU622
D	HIS651
D	THR653
D	ASP727
D	ALA729
D	ASN751
D	LEU752
D	HIS753
D	THR755
D	PHE756
D	GOL1105
D	HOH1249
D	HOH1429

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	16
Details	MOD_RES: N6-acetyllysine => ECO:0000250\|UniProtKB:Q91W43

Chain	Residue	Details
A	LYS447
A	LYS514
A	LYS648
A	LYS664
B	LYS447
B	LYS514
B	LYS648
B	LYS664
C	LYS447
C	LYS514
C	LYS648
C	LYS664
D	LYS447
D	LYS514
D	LYS648
D	LYS664

site_id	SWS_FT_FI2
Number of Residues	4
Details	MOD_RES: N6-(pyridoxal phosphate)lysine => ECO:0000250\|UniProtKB:P15505

Chain	Residue	Details
A	LYS754
B	LYS754
C	LYS754
D	LYS754

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)