Structure of PDB 6fbd Chain A

Receptor sequence

>6fbdA (length=539) Species: 271 (Thermus aquaticus) [Search protein sequence]

LEEAPWPPPEGAFVGFVLSRKEPMWADLLALAAARGGRVHRAPEPYKALR
DLKEARGLLAKDLSVLALREGLGLPPGDDPMLLAYLLDPSNTTPEGVARR
YGGEWTEEAGERAALSERLFANLWGRLEGEERLLWLYREVERPLSAVLAH
MEATGVRLDVAYLRALSLEVAEEIARLEAEVFRLAGHPFNLNSRDQLERV
LFDELGLPAIGKTEKTGKRSTSAAVLEALREAHPIVEKILQYRELTKLKS
TYIDPLPDLIHPRTGRLHTRFNQTATATGRLSSSDPNLQNIPVRTPLGQR
IRRAFIAEEGWLLVALDYSQIELRVLAHLSGDENLIRVFQEGRDIHTETA
SWMFGVPREAVDPLMRRAAKTINFGVLYGMSAHRLSQELAIPYEEAQAFI
ERYFQSFPKVRAWIEKTLEEGRRRGYVETLFGRRRYVPDLEARVKSVREA
AERMAFNMPVQGTAADLMKLAMVKLFPRLEEMGARMLLQVHDELVLEAPK
ERAEAVARLAKEVMEGVYPLAVPLEVEVGIGEDWLSAKE

3D structure

PDB

6fbd Snapshots of a modified nucleotide moving through the confines of a DNA polymerase.

Chain

Resolution

2.099 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 N583 I584 P585 V586 R587 R595 R660 V783 H784 D785	R194 T213 K215 T216 S220 T221 S222 A223 R243 K247 Y252 R280 N290 I291 P292 V293 R294 R302 R367 V490 H491 D492
BS02	dna	A	N483 N485 S486 S513 S515 A517 V518 S543 T544 T569 A570 T571 R573 S575 S576 S577 D578 N580 F667 G668 Y671 M673 S674 R677 R728 R746 M747 N750 Q754	N190 N192 S193 S220 S222 A224 V225 S250 T251 T276 A277 T278 R280 S282 S283 S284 D285 N287 F374 G375 Y378 M380 S381 R384 R435 R453 M454 N457 Q461
BS03	MN	A	D610 D785 E786	D317 D492 E493
BS04	MN	A	D610 Y611 D785	D317 Y318 D492
BS05	XG4	A	R573 D610 Y611 Q613 I614 E615 H639 R659 K663 F667 D785	R280 D317 Y318 Q320 I321 E322 H346 R366 K370 F374 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:6fbd, PDBe:6fbd, PDBj:6fbd
PDBsum	6fbd
PubMed	30224478
UniProt	P19821\|DPO1_THEAQ DNA polymerase I, thermostable (Gene Name=polA)

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