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5FW1

Crystal structure of SpyCas9 variant VQR bound to sgRNA and TGAG PAM target DNA

Functional Information from GO Data
ChainGOidnamespacecontents
B0003677molecular_functionDNA binding
B0003723molecular_functionRNA binding
B0004518molecular_functionnuclease activity
B0004519molecular_functionendonuclease activity
B0004520molecular_functionDNA endonuclease activity
B0004527molecular_functionexonuclease activity
B0008408molecular_function3'-5' exonuclease activity
B0016787molecular_functionhydrolase activity
B0043571biological_processmaintenance of CRISPR repeat elements
B0046872molecular_functionmetal ion binding
B0051607biological_processdefense response to virus
Functional Information from PDB Data
site_idAC1
Number of Residues4
DetailsBINDING SITE FOR RESIDUE MG A 2083
ChainResidue
AHOH3027
AHOH3028
AHOH3100
BK3374

site_idAC2
Number of Residues5
DetailsBINDING SITE FOR RESIDUE MG A 2084
ChainResidue
AU50
AHOH3058
AHOH3059
AHOH3060
AHOH3069

site_idAC3
Number of Residues3
DetailsBINDING SITE FOR RESIDUE K B 3365
ChainResidue
AA68
AHOH3091
BGLN1350

site_idAC4
Number of Residues4
DetailsBINDING SITE FOR RESIDUE K B 3366
ChainResidue
BGLU584
BARG586
BASN588
BHOH3093

site_idAC5
Number of Residues4
DetailsBINDING SITE FOR RESIDUE K B 3367
ChainResidue
AA65
AU66
AHOH3083
BTHR1102

site_idAC6
Number of Residues2
DetailsBINDING SITE FOR RESIDUE K B 3374
ChainResidue
AG21
AMG2083

site_idAC7
Number of Residues4
DetailsBINDING SITE FOR RESIDUE K B 3368
ChainResidue
BLEU623
BTHR624
BPHE626
BTYR656

site_idAC8
Number of Residues5
DetailsBINDING SITE FOR RESIDUE K B 3369
ChainResidue
BGLY361
BTYR362
BGLY365
BGLY366
BALA367

site_idAC9
Number of Residues6
DetailsBINDING SITE FOR RESIDUE K B 3370
ChainResidue
BILE226
BLEU229
BPRO230
BGLY231
BGLU232
BHOH3043

site_idBC1
Number of Residues4
DetailsBINDING SITE FOR RESIDUE K B 3371
ChainResidue
BGLU108
BLYS111
BHOH3027
BHOH3028

site_idBC2
Number of Residues4
DetailsBINDING SITE FOR RESIDUE K B 3372
ChainResidue
BASP576
BSER577
BALA640
BPHE643

site_idBC3
Number of Residues2
DetailsBINDING SITE FOR RESIDUE K A 2082
ChainResidue
AU22
BGLY365

site_idBC4
Number of Residues2
DetailsBINDING SITE FOR RESIDUE K B 3373
ChainResidue
BGLU57
BHOH3017

site_idBC5
Number of Residues2
DetailsBINDING SITE FOR RESIDUE K A 2081
ChainResidue
AU12
AG13

site_idBC6
Number of Residues2
DetailsBINDING SITE FOR RESIDUE K D 2013
ChainResidue
DDT5
DHOH3002

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues17
DetailsRegion: {"description":"ARM","evidences":[{"source":"PubMed","id":"24505130","evidenceCode":"ECO:0000303"}]}
ChainResidueDetails

site_idSWS_FT_FI2
Number of Residues2
DetailsMotif: {"description":"PAM substrate-binding","evidences":[{"source":"PubMed","id":"25079318","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails

site_idSWS_FT_FI3
Number of Residues1
DetailsActive site: {"description":"For RuvC-like nuclease domain","evidences":[{"source":"PubMed","id":"24529477","evidenceCode":"ECO:0000305"}]}
ChainResidueDetails

site_idSWS_FT_FI4
Number of Residues1
DetailsActive site: {"description":"Proton acceptor for HNH nuclease domain","evidences":[{"source":"PubMed","id":"24529477","evidenceCode":"ECO:0000305"}]}
ChainResidueDetails

site_idSWS_FT_FI5
Number of Residues5
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"24505130","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails

246704

PDB entries from 2025-12-24

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