Structure of PDB 5ytd Chain A

Receptor sequence

>5ytdA (length=539) Species: 271 (Thermus aquaticus) [Search protein sequence]

LEEAPWPPPEGAFVGFVLSRKEPMWADLLALAAARGGRVHRAPEPYKALR
DLKEARGLLAKDLSVLALREGLGLPPGDDPMLLAYLLDPSNTTPEGVARR
YGGEWTEEAGERAALSERLFANLWGRLEGEERLLWLYREVERPLSAVLAH
MEATGVRLDVAYLRALSLEVAEEIARLEAEVFRLAGHPFNLNSRDQLERV
LFDELGLPAIGKTEKTGKRSTSAAVLEALREAHPIVEKILQYRELTKLKS
TYIDPLPDLIHPRTGRLHTRFNQTATATGRLSSSDPNLQNIPVRTPLGQR
IRRAFIAEEGWLLVALDYSQIELRVLAHLSGDENLIRVFQEGRDIHTETA
SWMFGVPREAVDPLMRRAAKTINFGVLYGMSAHRLSQELAIPYEEAQAFI
ERYFQSFPKVRAWIEKTLEEGRRRGYVETLFGRRRYVPDLEARVKSVREA
AERMAFNMPVQGTAADLMKLAMVKLFPRLEEMGARMLLQVHDELVLEAPK
ERAEAVARLAKEVMEGVYPLAVPLEVEVGIGEDWLSAKE

3D structure

PDB

5ytd Unnatural Cytosine Bases Recognized as Thymines by DNA Polymerases by the Formation of the Watson-Crick Geometry.

Chain

Resolution

2.0 Å

3D
structure

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Enzymatic activity

Enzyme Commision number

2.7.7.7: DNA-directed DNA polymerase.

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)
BS01	dna	A	R487 T506 K508 T509 S513 T514 S515 A516 R536 K540 Y545 R573 Q582 N583 I584 P585 R587 H784	R194 T213 K215 T216 S220 T221 S222 A223 R243 K247 Y252 R280 Q289 N290 I291 P292 R294 H491
BS02	dna	A	N483 N485 S486 G504 K505 S513 V518 S543 T569 A570 T571 R573 S575 S576 S577 D578 N580 F667 G668 Y671 M673 S674 R677 Q680 R728 R746 M747 N750 Q754	N190 N192 S193 G211 K212 S220 V225 S250 T276 A277 T278 R280 S282 S283 S284 D285 N287 F374 G375 Y378 M380 S381 R384 Q387 R435 R453 M454 N457 Q461
BS03	DGT	A	R573 D610 Y611 S612 Q613 I614 E615 H639 R659 R660 K663 F667 Y671 D785	R280 D317 Y318 S319 Q320 I321 E322 H346 R366 R367 K370 F374 Y378 D492
BS04	MG	A	D610 Y611 D785	D317 Y318 D492
BS05	MG	A	D610 D785	D317 D492

Gene Ontology

	Molecular Function
GO:0001882	nucleoside binding
GO:0003676	nucleic acid binding
GO:0003677	DNA binding
GO:0003887	DNA-directed DNA polymerase activity

	Biological Process
GO:0006260	DNA replication
GO:0006261	DNA-templated DNA replication
GO:0006281	DNA repair

View graph for
Molecular Function

View graph for
Biological Process

External links

PDB	RCSB:5ytd, PDBe:5ytd, PDBj:5ytd
PDBsum	5ytd
PubMed	30407705
UniProt	P19821\|DPO1_THEAQ DNA polymerase I, thermostable (Gene Name=polA)

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