Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3FDE

Mouse UHRF1 SRA domain bound with hemi-methylated CpG DNA, crystal structure in space group C222(1) at 1.4 A resolution

Functional Information from PDB Data

site_id	AC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO A 629

Chain	Residue
A	ASN479
A	ARG586
A	ASP587
A	ASP588
A	HOH662
C	UNL359

site_id	AC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO A 630

Chain	Residue
A	LYS564
A	HOH857
A	HOH286
A	HOH374
A	PRO536

site_id	AC3
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO A 631

Chain	Residue
A	HOH42
A	ASP476
A	GLY545
A	GLY546
A	HOH651
A	HOH653
A	HOH700

site_id	AC4
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO A 632

Chain	Residue
A	SER549
A	LYS550
A	TYR551
A	ALA552
A	ARG558
A	TRP594
A	LYS599

site_id	AC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO A 633

Chain	Residue
A	ASN459
A	ARG511
A	HOH682
B	HOH144
B	HOH325
B	PRO430

site_id	AC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO A 634

Chain	Residue
A	ASP460
A	LYS535
A	HOH661
B	ARG601
B	GLN604
B	HOH650

site_id	AC7
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO A 635

Chain	Residue
A	SER442
A	GLU443
A	ARG448
A	HOH756
A	HOH856
E	DA429
E	DT430

site_id	AC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO A 636

Chain	Residue
A	ASP530
A	TRP531
A	ARG532
A	GLN533

site_id	AC9
Number of Residues	6
Details	BINDING SITE FOR RESIDUE NA A 637

Chain	Residue
A	PRO449
A	HIS450
A	VAL451
A	ALA452
D	DG406
E	HOH115

site_id	BC1
Number of Residues	7
Details	BINDING SITE FOR RESIDUE UNL A 638

Chain	Residue
A	LEU515
A	ASN516
A	CYS517
A	HIS518
A	GLN533
A	GLY534
B	GLN604

site_id	BC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE UNL A 654

Chain	Residue
A	HOH410
A	ARG581
A	HOH813
B	ARG572
F	HOH835

site_id	BC3
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO B 629

Chain	Residue
A	THR602
A	ARG603
A	GLY606
A	LEU607
B	HOH267
B	GLU529
B	TRP531

site_id	BC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO B 630

Chain	Residue
B	HOH106
B	HOH141
B	ASP476
B	GLY545
B	HIS548

site_id	BC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO B 631

Chain	Residue
B	HOH102
B	HOH305
B	ARG586
B	ASP588
B	THR589
B	GLU590

site_id	BC6
Number of Residues	2
Details	BINDING SITE FOR RESIDUE EDO B 632

Chain	Residue
B	HOH671
C	HOH18

site_id	BC7
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO B 633

Chain	Residue
A	HOH212
A	GLU472
B	ARG572
B	GLY573
B	LYS574
B	GLY576

site_id	BC8
Number of Residues	5
Details	BINDING SITE FOR RESIDUE NA B 634

Chain	Residue
B	HIS450
B	VAL451
B	ALA452
C	DG406
F	HOH72

site_id	BC9
Number of Residues	5
Details	BINDING SITE FOR RESIDUE UNL B 655

Chain	Residue
B	ASN479
B	TYR480
B	ARG585
A	ARG603
A	GLN604

site_id	CC1
Number of Residues	12
Details	BINDING SITE FOR RESIDUE UNL B 322

Chain	Residue
B	HOH347
B	LEU515
B	ASN516
B	CYS517
B	HIS518
B	GLN533
B	GLY534
B	HOH660
B	HOH692
B	HOH694
D	DT405
D	DG406

site_id	CC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE UNL B 215

Chain	Residue
B	HOH335
B	ASP476
B	SER549
B	LYS550
B	TYR551

site_id	CC3
Number of Residues	8
Details	BINDING SITE FOR RESIDUE UNL B 636

Chain	Residue
B	GLY487
B	GLY488
B	ARG489
B	SER502
B	HOH638
C	HOH183
C	UNL456
C	UNL637

site_id	CC4
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO D 502

Chain	Residue
A	ASN509
D	DT405
E	HOH128
E	DT430
E	DG431
E	EDO501
E	NA504

site_id	CC5
Number of Residues	8
Details	BINDING SITE FOR RESIDUE EDO E 501

Chain	Residue
D	DA404
D	DT405
D	EDO502
E	DT430
E	DG431
E	DG432
E	NA504
E	HOH855

site_id	CC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO E 503

Chain	Residue
A	THR497
E	DC423
E	DA424
E	DG425
E	HOH446

site_id	CC7
Number of Residues	5
Details	BINDING SITE FOR RESIDUE NA E 504

Chain	Residue
D	EDO502
D	HOH621
E	DT430
E	DG431
E	EDO501

site_id	CC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO C 505

Chain	Residue
B	ASN509
C	DT405
F	HOH59
F	DT430
F	NA503
F	EDO506

site_id	CC9
Number of Residues	5
Details	BINDING SITE FOR RESIDUE UNL C 359

Chain	Residue
A	ASN479
A	ARG586
A	EDO629
C	HOH70
C	DC402

site_id	DC1
Number of Residues	7
Details	BINDING SITE FOR RESIDUE UNL C 456

Chain	Residue
B	GLY487
B	UNL636
C	HOH56
C	HOH183
C	DT405
C	DG406
C	UNL637

site_id	DC2
Number of Residues	8
Details	BINDING SITE FOR RESIDUE UNL C 637

Chain	Residue
B	ARG489
B	LEU491
B	UNL636
C	HOH113
C	HOH135
C	DT405
C	DG406
C	UNL456

site_id	DC3
Number of Residues	8
Details	BINDING SITE FOR RESIDUE EDO F 506

Chain	Residue
C	DA404
C	DT405
C	EDO505
F	HOH264
F	DT430
F	DG431
F	DG432
F	NA503

site_id	DC4
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO F 509

Chain	Residue
F	DG431
F	DG432
F	EDO510

site_id	DC5
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO F 510

Chain	Residue
A	VAL566
A	LEU583
A	ARG585
B	ARG457
F	HOH219
F	DG431
F	EDO509

site_id	DC6
Number of Residues	2
Details	BINDING SITE FOR RESIDUE EDO F 511

Chain	Residue
A	ARG585
F	DG431

site_id	DC7
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO F 513

Chain	Residue
B	THR497
B	HOH639
F	HOH327
F	DC423
F	DA424
F	DG425

site_id	DC8
Number of Residues	5
Details	BINDING SITE FOR RESIDUE NA F 503

Chain	Residue
C	HOH33
C	EDO505
F	DT430
F	DG431
F	EDO506

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	324
Details	Domain: {"description":"YDG","evidences":[{"source":"PROSITE-ProRule","id":"PRU00358","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	2
Details	Region: {"description":"Required to promote base flipping"}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	12
Details	Region: {"description":"Required for formation of a 5-methylcytosine-binding pocket"}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	4
Details	Binding site: {"evidences":[{"evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	2
Details	Site: {"description":"Required to confer preferential recognition of cytosine over thymine","evidences":[{"evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	2
Details	Site: {"description":"Required to discriminate between hemimethylated DNA versus symmetrically methylated DNA"}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	2
Details	Site: {"description":"Required for affinity and specificity for 5-mCpG sequence"}

Chain

Residue

Details

site_id	SWS_FT_FI8
Number of Residues	2
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"21183079","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI9
Number of Residues	2
Details	Modified residue: {"description":"N6-acetyllysine; alternate","evidences":[{"source":"UniProtKB","id":"Q96T88","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI10
Number of Residues	4
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternate","evidences":[{"source":"UniProtKB","id":"Q96T88","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

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