Structure of PDB 6r5d Chain A

Receptor sequence
>6r5dA (length=384) Species: 9606 (Homo sapiens) [Search protein sequence]
DPTELPELLKLYYRRLFPYSQYYRWLNYGGVIKNYFQHREFSFTLKDDIY
IRYQSFNNQSDLEKEMQKMNPYKIDIGAVYSHRPNQHNTVKLGAFQAQEK
ELVFDIDMTDYDDVRRCCSSADICPKCWTLMTMAIRIIDRALKEDFGFKH
RLWVYSGRRGVHCWVCDESVRKLSSAVRSGIVEYLSLVKGGQDVKKKVHL
SEKIHPFIRKSINIIKKYFEEYALVNQDILENKESWDKILALVPETIHDE
LQQSFQKSHNSLQRWEHLKKVASRYQNNIKNDKYGPWLEWEIMLQYCFPR
LDINVSKGINHLLKSPFSVHPKTGRISVPIDLQKVDQFDPFTVPTISFIC
RELDAITRDYKKTSLAPYVKVFEHFLENLDKSRK
3D structure
PDB6r5d Structural Basis for Inhibition of Human Primase by Arabinofuranosyl Nucleoside Analogues Fludarabine and Vidarabine.
ChainA
Resolution1.95 Å
3D
structure
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Enzymatic activity
Enzyme Commision number 2.7.7.102: DNA primase AEP.
Interaction with ligand
Site
#		 Ligand Ligand
chain		 Binding residues on receptor
(original residue number in PDB)		 Binding residues on receptor
(residue number reindexed from 1)		 Binding affinity
BS01 ZN A C121 C122 C128 C131 C117 C118 C124 C127
BS02 MN A D109 D111 D105 D107
BS03 MN A D109 D111 D306 D105 D107 D302
BS04 DTP A D109 D111 S160 R162 R163 H166 L316 L317 K318 H324 D105 D107 S156 R158 R159 H162 L312 L313 K314 H320
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0003896 DNA primase activity
GO:0005515 protein binding
GO:0008270 zinc ion binding
GO:0016779 nucleotidyltransferase activity
GO:0032553 ribonucleotide binding
GO:0046872 metal ion binding
Biological Process
GO:0006260 DNA replication
GO:0006269 DNA replication, synthesis of primer
GO:0006270 DNA replication initiation
Cellular Component
GO:0000428 DNA-directed RNA polymerase complex
GO:0005654 nucleoplasm
GO:0005658 alpha DNA polymerase:primase complex
GO:0016020 membrane
GO:1990077 primosome complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6r5d, PDBe:6r5d, PDBj:6r5d
PDBsum6r5d
PubMed31479243
UniProtP49642|PRI1_HUMAN DNA primase small subunit (Gene Name=PRIM1)

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