Structure of PDB 6i34 Chain C Binding Site BS01

Receptor Information
>6i34 Chain C (length=953) Species: 63221 (Homo sapiens neanderthalensis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ASRLLERLLPRHDDFARRHIGPGDKDQREMLQTLGLASIDELIEKTVPAN
IRLKRPLKMEDPVCENEILATLHAISSKNQIWRSYIGMGYYNCSVPQTIL
RNLLENSGWITQYTPYQPEVSQGRLESLLNYQTMVCDITGLDMANASLLD
EGTAAAEALQLCYRHNKRRKFFVDPRCHPQTIAVVQTRAKYTGVLTELKL
PCEMDFSGKDVSGVLFQYPDTEGKVEDFTELVERAHQSGSLACCATDLLA
LCILRPPGEFGVDIALGSSQRFGVPLGYGGPHAAFFAVRESLVRMMPGRM
VGVTRDATGKEVYRLALQTREQHIRRDKATSNICTAQALLANMAAMFAIY
HGSHGLEHIARRVHNATLILSEGLKRAGHQLQHDLFFDTLKIQCGCSVKE
VLGRAAQRQINFRLFEDGTLGISLDETVNEKDLDDLLWIFGCESSAELVA
ESMRGIPGSVFKRTSPFLTHQVFNSYHSETNIVRYMKKLENKDISLVHSM
IPLGSCTMKLNSSSELAPITWKEFANIHPFVPLDQAQGYQQLFRELEKDL
CELTGYDQVCFQPNSGAQGEYAGLATIRAYLNQKGEGHRTVCLIPKSAHG
TNPASAHMAGMKIQPVEVDKYGNIDAVHLKAMVDKHKENLAAIMITYPST
NGVFEENISDVCDLIHQHGGQVYLDGANMNAQVGICRPGDFGSDVSHLNL
HKTFCIPHGGGGPGMGPIGVKKHLAPFLPNHPVISLKRNEDACPVGTVSA
APWGSSSILPISWAYIKMMGGKGLKQATETAILNANYMAKRLETHYRILF
RGARGYVGHEFILDTRPFKKSANIEAVDVAKRLQDYGFHAPTMSWPVAGT
LMVEPTESEDKAELDRFCDAMISIRQEIADIEEGRIDPRVNPLKMSPHSL
TCVTSSHWDRPYSREVAAFPLPFVKPENKFWPTIARIDDIYGDQHLVCTC
PPM
Ligand information
Ligand IDPLP
InChIInChI=1S/C8H10NO6P/c1-5-8(11)7(3-10)6(2-9-5)4-15-16(12,13)14/h2-3,11H,4H2,1H3,(H2,12,13,14)
InChIKeyNGVDGCNFYWLIFO-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Cc1ncc(CO[P](O)(O)=O)c(C=O)c1O
OpenEye OEToolkits 1.5.0Cc1c(c(c(cn1)COP(=O)(O)O)C=O)O
ACDLabs 10.04O=P(O)(O)OCc1cnc(c(O)c1C=O)C
FormulaC8 H10 N O6 P
NamePYRIDOXAL-5'-PHOSPHATE;
VITAMIN B6 Phosphate
ChEMBLCHEMBL82202
DrugBankDB00114
ZINCZINC000001532514
PDB chain6i34 Chain C Residue 1101 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6i34 Structural insights in human glycine decarboxylase and comparison with the Neanderthal variant
Resolution2.1 Å
Binding residue
(original residue number in PDB)		C382 T383 S557 G618 A619 H651 D727 A729 N751 H753 K754
Binding residue
(residue number reindexed from 1)		C334 T335 S505 G566 A567 H599 D675 A677 N699 H701 K702
Annotation score1
Enzymatic activity
Enzyme Commision number 1.4.4.2: glycine dehydrogenase (aminomethyl-transferring).
Gene Ontology
Molecular Function
GO:0004375 glycine dehydrogenase (decarboxylating) activity
GO:0009055 electron transfer activity
GO:0016491 oxidoreductase activity
GO:0016594 glycine binding
GO:0016829 lyase activity
GO:0030170 pyridoxal phosphate binding
GO:0042803 protein homodimerization activity
GO:0070280 pyridoxal binding
Biological Process
GO:0006520 amino acid metabolic process
GO:0006544 glycine metabolic process
GO:0006546 glycine catabolic process
GO:0019464 glycine decarboxylation via glycine cleavage system
GO:0036255 response to methylamine
GO:1903442 response to lipoic acid
GO:1990830 cellular response to leukemia inhibitory factor
Cellular Component
GO:0005654 nucleoplasm
GO:0005739 mitochondrion
GO:0005759 mitochondrial matrix
GO:0005886 plasma membrane
GO:0005960 glycine cleavage complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6i34, PDBe:6i34, PDBj:6i34
PDBsum6i34
PubMed
UniProtP23378|GCSP_HUMAN Glycine dehydrogenase (decarboxylating), mitochondrial (Gene Name=GLDC)

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