Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

6DWJ

SAMHD1 Bound to Vidarabine-TP in the Catalytic Pocket

Functional Information from PDB Data

site_id	AC1
Number of Residues	21
Details	binding site for residue HEJ D 701

Chain	Residue
D	GLN149
D	TYR315
D	ASP319
D	ARG366
D	HIS370
D	TYR374
D	GLN375
D	MG706
D	HOH806
D	HOH807
D	HOH818
D	LEU150
D	HOH825
D	HOH833
D	ARG164
D	ARG206
D	HIS210
D	HIS215
D	HIS233
D	ASP311
D	LYS312

site_id	AC2
Number of Residues	18
Details	binding site for residue GTP D 702

Chain	Residue
A	LYS116
A	VAL117
A	ILE118
A	ILE136
A	ASP137
A	GLN142
A	ARG145
A	PHE165
A	MG701
A	HOH824
B	LYS523
B	DTP701
D	TYR155
D	VAL156
D	VAL378
D	ARG451
D	LYS455
D	HOH829

site_id	AC3
Number of Residues	15
Details	binding site for residue DTP D 703

Chain	Residue
B	VAL156
B	PHE157
B	ARG372
B	HIS376
B	LYS377
B	GTP704
C	VAL117
C	ASN119
C	MG703
D	ARG333
D	PHE337
D	ARG352
D	LYS354
D	ASN358
D	LYS523

site_id	AC4
Number of Residues	3
Details	binding site for residue MG D 704

Chain	Residue
C	DTP704
D	LYS116
D	GTP705

site_id	AC5
Number of Residues	17
Details	binding site for residue GTP D 705

Chain	Residue
A	TYR155
A	VAL156
A	VAL378
A	ARG451
A	LYS455
C	LYS523
C	DTP704
D	LYS116
D	VAL117
D	ILE118
D	ILE136
D	ASP137
D	GLN142
D	ARG145
D	PHE165
D	MG704
D	HOH816

site_id	AC6
Number of Residues	6
Details	binding site for residue MG D 706

Chain	Residue
D	ASP309
D	LYS312
D	HEJ701
D	HOH807
D	HOH818
D	HOH825

site_id	AC7
Number of Residues	4
Details	binding site for residue MG D 707

Chain	Residue
D	GLN149
D	LEU150
D	ALA160
D	HIS162

site_id	AC8
Number of Residues	4
Details	binding site for residue NA D 708

Chain	Residue
D	HIS210
D	GLY211
D	SER214
D	ASP218

site_id	AC9
Number of Residues	4
Details	binding site for residue NA D 709

Chain	Residue
D	HIS123
D	TYR331
D	LYS332
D	HOH817

site_id	AD1
Number of Residues	7
Details	binding site for residue NA D 710

Chain	Residue
A	HIS162
A	GLU166
A	HIS322
A	HOH822
D	PRO158
D	GLY159
D	SER161

site_id	AD2
Number of Residues	2
Details	binding site for residue NA D 711

Chain	Residue
D	PRO130
D	HOH852

site_id	AD3
Number of Residues	19
Details	binding site for residue HEJ C 701

Chain	Residue
C	GLN149
C	LEU150
C	ARG164
C	ARG206
C	HIS210
C	HIS215
C	HIS233
C	ASP311
C	LYS312
C	TYR315
C	ASP319
C	ARG366
C	TYR374
C	GLN375
C	MG705
C	HOH803
C	HOH813
C	HOH819
C	HOH820

site_id	AD4
Number of Residues	17
Details	binding site for residue GTP C 702

Chain	Residue
A	LYS523
A	DTP702
B	LYS116
B	VAL117
B	ILE118
B	ASP137
B	GLN142
B	ARG145
B	PHE165
B	MG702
C	TYR155
C	VAL156
C	VAL378
C	ARG451
C	LYS455
C	HOH805
C	HOH828

site_id	AD5
Number of Residues	3
Details	binding site for residue MG C 703

Chain	Residue
B	GTP704
C	LYS116
D	DTP703

site_id	AD6
Number of Residues	16
Details	binding site for residue DTP C 704

Chain	Residue
A	VAL156
A	PHE157
A	ARG372
A	HIS376
A	LYS377
C	ARG333
C	PHE337
C	ARG352
C	LYS354
C	ASN358
C	LYS523
C	HOH809
D	VAL117
D	ASN119
D	MG704
D	GTP705

site_id	AD7
Number of Residues	6
Details	binding site for residue MG C 705

Chain	Residue
C	ASP309
C	LYS312
C	HEJ701
C	HOH803
C	HOH813
C	HOH819

site_id	AD8
Number of Residues	6
Details	binding site for residue NA C 706

Chain	Residue
B	HIS162
B	GLU166
B	HIS322
C	PRO158
C	GLY159
C	SER161

site_id	AD9
Number of Residues	1
Details	binding site for residue NA C 707

Chain	Residue
C	ALA317

site_id	AE1
Number of Residues	5
Details	binding site for residue NA C 708

Chain	Residue
C	TYR507
C	MET509
C	GLN510
C	LYS512
C	PHE545

site_id	AE2
Number of Residues	2
Details	binding site for residue NA C 709

Chain	Residue
C	ARG366
C	ASP506

site_id	AE3
Number of Residues	16
Details	binding site for residue DTP B 701

Chain	Residue
A	VAL117
A	ASN119
A	MG701
B	ARG333
B	PHE337
B	ARG352
B	LYS354
B	ASN358
B	LYS523
B	HOH817
D	VAL156
D	PHE157
D	ARG372
D	HIS376
D	LYS377
D	GTP702

site_id	AE4
Number of Residues	3
Details	binding site for residue MG B 702

Chain	Residue
A	DTP702
B	LYS116
C	GTP702

site_id	AE5
Number of Residues	21
Details	binding site for residue HEJ B 703

Chain	Residue
B	GLN149
B	LEU150
B	ARG164
B	ARG206
B	HIS210
B	HIS215
B	HIS233
B	ASP311
B	LYS312
B	TYR315
B	ASP319
B	ARG366
B	HIS370
B	TYR374
B	GLN375
B	MG705
B	HOH801
B	HOH809
B	HOH814
B	HOH828
B	HOH830

site_id	AE6
Number of Residues	18
Details	binding site for residue GTP B 704

Chain	Residue
B	TYR155
B	VAL156
B	VAL378
B	ARG451
B	LYS455
B	HOH811
B	HOH826
C	LYS116
C	VAL117
C	ILE118
C	ASP137
C	GLN142
C	ARG145
C	PHE165
C	MG703
C	HOH823
D	LYS523
D	DTP703

site_id	AE7
Number of Residues	4
Details	binding site for residue MG B 705

Chain	Residue
B	ASP309
B	LYS312
B	HEJ703
B	HOH809

site_id	AE8
Number of Residues	2
Details	binding site for residue NA B 706

Chain	Residue
B	HIS364
B	TYR507

site_id	AE9
Number of Residues	4
Details	binding site for residue NA B 707

Chain	Residue
B	GLN149
B	LEU150
B	ALA160
B	HIS162

site_id	AF1
Number of Residues	3
Details	binding site for residue NA B 708

Chain	Residue
B	TYR360
B	TYR507
B	PRO542

site_id	AF2
Number of Residues	3
Details	binding site for residue NA B 709

Chain	Residue
B	GLU299
B	ASN303
B	ASN306

site_id	AF3
Number of Residues	5
Details	binding site for residue GLY B 710

Chain	Residue
B	ARG371
B	ARG372
D	GLY357
D	ASN358
D	ASP361

site_id	AF4
Number of Residues	1
Details	binding site for residue PO4 B 711

Chain	Residue
B	HIS517

site_id	AF5
Number of Residues	3
Details	binding site for residue MG A 701

Chain	Residue
A	LYS116
B	DTP701
D	GTP702

site_id	AF6
Number of Residues	15
Details	binding site for residue DTP A 702

Chain	Residue
A	ARG333
A	PHE337
A	ARG352
A	LYS354
A	ASN358
A	LYS523
B	VAL117
B	ASN119
B	MG702
C	VAL156
C	PHE157
C	ARG372
C	HIS376
C	LYS377
C	GTP702

site_id	AF7
Number of Residues	19
Details	binding site for residue HEJ A 703

Chain	Residue
A	GLN149
A	LEU150
A	ARG164
A	ARG206
A	HIS210
A	HIS215
A	HIS233
A	ASP311
A	LYS312
A	TYR315
A	ASP319
A	ARG366
A	TYR374
A	GLN375
A	MG705
A	HOH801
A	HOH806
A	HOH823
A	HOH825

site_id	AF8
Number of Residues	4
Details	binding site for residue MG A 704

Chain	Residue
A	GLN149
A	LEU150
A	ALA160
A	HIS162

site_id	AF9
Number of Residues	5
Details	binding site for residue MG A 705

Chain	Residue
A	ASP309
A	LYS312
A	HEJ703
A	HOH801
A	HOH806

site_id	AG1
Number of Residues	7
Details	binding site for residue NA A 706

Chain	Residue
A	PHE157
A	PRO158
A	GLY159
A	HIS322
A	LEU323
D	ASN119
D	PRO121

site_id	AG2
Number of Residues	1
Details	binding site for residue NA A 707

Chain	Residue
A	ALA317

site_id	AG3
Number of Residues	7
Details	binding site for residue NA A 708

Chain	Residue
A	PRO158
A	GLY159
A	SER161
D	HIS162
D	GLU166
D	HIS322
D	HOH831

site_id	AG4
Number of Residues	2
Details	binding site for residue NA A 709

Chain	Residue
A	HIS123
A	TYR331

site_id	AG5
Number of Residues	4
Details	binding site for residue NA A 710

Chain	Residue
A	ARG531
A	GLN536
C	LYS580
C	GLN582

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	4
Details	Active site: {"evidences":[{"source":"PubMed","id":"22056990","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	20
Details	Binding site: {"description":"in chain B","evidences":[{"source":"PubMed","id":"25267621","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"4TNP","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4TNQ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4TNR","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4TNX","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	4
Details	Binding site: {"description":"in chain B","evidences":[{"source":"PubMed","id":"25267621","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"4TNQ","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	32
Details	Binding site: {"evidences":[{"source":"PubMed","id":"25267621","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"4TNQ","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	28
Details	Binding site: {"evidences":[{"source":"PubMed","id":"24141705","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"4BZB","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	16
Details	Binding site: {"description":"in chain C","evidences":[{"source":"PubMed","id":"25267621","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"4TNQ","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	12
Details	Binding site: {"description":"in chain A","evidences":[{"source":"PubMed","id":"25267621","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"4TNQ","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI8
Number of Residues	4
Details	Binding site: {"description":"in chain A","evidences":[{"source":"PubMed","id":"24141705","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"25267621","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"4BZB","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4TNX","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI9
Number of Residues	8
Details	Binding site: {"description":"in chain C","evidences":[{"source":"PubMed","id":"25267621","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"4TNP","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4TNQ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4TNR","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4TNX","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI10
Number of Residues	4
Details	Binding site: {"description":"in chain A","evidences":[{"source":"PubMed","id":"25267621","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"4TNP","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4TNQ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4TNR","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4TNX","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI11
Number of Residues	4
Details	Modified residue: {"description":"Phosphothreonine; by CDK1","evidences":[{"source":"PubMed","id":"23601106","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"23602554","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"26294762","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"26431200","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"29610582","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"29670289","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"17081983","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"18669648","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"18691976","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"19369195","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"20068231","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"24275569","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI12
Number of Residues	16
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)","evidences":[{"source":"PubMed","id":"28112733","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

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