6WE9

YTH domain of human YTHDC1 with 11mer ssDNA Containing N6mA

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0003723	molecular_function	RNA binding
C	0003723	molecular_function	RNA binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	7
Details	binding site for residue EDO A 601

Chain	Residue
A	HIS365
A	SER369
A	LYS372
A	GLN410
A	EDO604
A	HOH706
A	HOH762

---

site_id	AC2
Number of Residues	4
Details	binding site for residue EDO A 602

Chain	Residue
A	HOH701
A	HOH719
A	HIS420
A	HIS421

---

site_id	AC3
Number of Residues	4
Details	binding site for residue SO4 A 603

Chain	Residue
A	ASN363
A	PRO431
A	ALA432
A	HOH708

---

site_id	AC4
Number of Residues	7
Details	binding site for residue EDO A 604

Chain	Residue
A	HIS365
A	SER406
A	LYS408
A	GLN410
A	ARG451
A	GLU452
A	EDO601

---

site_id	AC5
Number of Residues	2
Details	binding site for residue EDO A 605

Chain	Residue
A	ARG404
A	ARG475

---

site_id	AC6
Number of Residues	3
Details	binding site for residue EDO A 607

Chain	Residue
A	PHE391
A	ARG392
A	ALA394

---

site_id	AC7
Number of Residues	5
Details	binding site for residue GOL A 608

Chain	Residue
A	ARG475
A	ASP476
A	GLY477
A	GLN478
A	HOH704

---

site_id	AC8
Number of Residues	5
Details	binding site for residue GOL A 609

Chain	Residue
A	LEU461
A	THR462
A	GLU481
A	GLU483
A	CYS484

---

site_id	AC9
Number of Residues	2
Details	binding site for residue EDO A 610

Chain	Residue
A	TRP465
B	HOH105

---

site_id	AD1
Number of Residues	27
Details	binding site for Di-nucleotide DG B 5 and 6MA B 6

Chain	Residue
A	LYS361
A	SER362
A	ASN363
A	ASN367
A	TRP377
A	SER378
A	LEU380
A	PRO381
A	TRP428
A	HIS468
A	ASP476
A	HOH710
A	HOH764
A	HOH781
B	DC3
B	DG4
B	DC7
B	HOH103
B	HOH105
B	HOH107
B	HOH108
B	HOH109
B	HOH111
B	HOH113
B	HOH114
B	HOH117
B	HOH119

---

site_id	AD2
Number of Residues	23
Details	binding site for Di-nucleotide 6MA B 6 and DC B 7

Chain	Residue
A	LYS361
A	SER362
A	ASN363
A	ASN367
A	TRP377
A	SER378
A	LEU380
A	TRP428
A	ILE473
A	GLY474
A	ARG475
A	ASP476
A	HOH710
A	HOH739
A	HOH764
A	HOH781
B	DG5
B	DT8
B	HOH104
B	HOH110
B	HOH113
B	HOH115
B	HOH117

---

site_id	AD3
Number of Residues	13
Details	binding site for Di-nucleotide DG F 5 and 6MA F 6

Chain	Residue
C	ASP476
F	DG4
F	DC7
B	DT10
B	DG11
C	LYS361
C	ASN363
C	TRP377
C	SER378
C	THR379
C	ALA432
C	GLY433
C	MET438

---

site_id	AD4
Number of Residues	12
Details	binding site for Di-nucleotide 6MA F 6 and DC F 7

Chain	Residue
C	LYS361
C	ASN363
C	TRP377
C	SER378
C	THR379
C	ILE473
C	GLY474
C	ARG475
C	ASP476
F	DG5
F	DT8
F	HOH103

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	274
Details	Domain: {"description":"YTH","evidences":[{"source":"PROSITE-ProRule","id":"PRU00225","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
Number of Residues	6
Details	Binding site: {"evidences":[{"source":"PubMed","id":"31670957","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"6RT4","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"6RT5","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"6RT6","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"6RT7","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI3
Number of Residues	2
Details	Binding site: {"evidences":[{"source":"PubMed","id":"25242552","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"31670957","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"6RT4","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"6RT5","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"6RT6","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"6RT7","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI4
Number of Residues	2
Details	Binding site: {"evidences":[{"source":"PubMed","id":"25242552","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI5
Number of Residues	2
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"18669648","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"20068231","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI6
Number of Residues	2
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"20068231","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---