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6JB8

Crystal structure of nanobody D3-L11 in complex with hen egg-white lysozyme

Functional Information from GO Data
ChainGOidnamespacecontents
B0003796molecular_functionlysozyme activity
B0003824molecular_functioncatalytic activity
B0005515molecular_functionprotein binding
B0005576cellular_componentextracellular region
B0005615cellular_componentextracellular space
B0005737cellular_componentcytoplasm
B0005783cellular_componentendoplasmic reticulum
B0016231molecular_functionbeta-N-acetylglucosaminidase activity
B0016787molecular_functionhydrolase activity
B0016798molecular_functionhydrolase activity, acting on glycosyl bonds
B0016998biological_processcell wall macromolecule catabolic process
B0031640biological_processkilling of cells of another organism
B0042742biological_processdefense response to bacterium
B0042802molecular_functionidentical protein binding
B0050829biological_processdefense response to Gram-negative bacterium
B0050830biological_processdefense response to Gram-positive bacterium
B0051672biological_processobsolete catabolism by organism of cell wall peptidoglycan in other organism
Functional Information from PDB Data
site_idAC1
Number of Residues4
Detailsbinding site for residue NO3 A 201
ChainResidue
ASER27
ATHR28
AASP29
AHOH339

site_idAC2
Number of Residues3
Detailsbinding site for residue NA A 202
ChainResidue
ASER27
ASER30
AHOH363

site_idAC3
Number of Residues10
Detailsbinding site for residue GOL B 201
ChainResidue
BILE58
BASN59
BTRP63
BALA107
BTRP108
BNA204
BHOH343
BHOH349
ATYR102
BGLN57

site_idAC4
Number of Residues2
Detailsbinding site for residue GOL B 202
ChainResidue
BTYR20
BARG21

site_idAC5
Number of Residues6
Detailsbinding site for residue NA B 203
ChainResidue
BSER60
BCYS64
BSER72
BARG73
BHOH381
BHOH390

site_idAC6
Number of Residues5
Detailsbinding site for residue NA B 204
ChainResidue
BGLU35
BGLN57
BGOL201
BHOH341
BHOH349

site_idAC7
Number of Residues3
Detailsbinding site for residue CL B 205
ChainResidue
AGLN3
BILE88
BHOH432

Functional Information from PROSITE/UniProt
site_idPS00128
Number of Residues19
DetailsGLYCOSYL_HYDROL_F22_1 Glycosyl hydrolases family 22 (GH22) domain signature. CnipCsaLlssDItasvnC
ChainResidueDetails
BCYS76-CYS94

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues128
DetailsDomain: {"description":"C-type lysozyme","evidences":[{"source":"PROSITE-ProRule","id":"PRU00680","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails

site_idSWS_FT_FI2
Number of Residues2
DetailsActive site: {}
ChainResidueDetails

site_idSWS_FT_FI3
Number of Residues1
DetailsBinding site: {}
ChainResidueDetails

Catalytic Information from CSA
site_idMCSA1
Number of Residues6
DetailsM-CSA 203
ChainResidueDetails
BGLU35hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
BASN46
BASP48
BSER50
BASP52covalently attached, electrostatic stabiliser, nucleofuge, nucleophile, polar/non-polar interaction
BASN59

238895

PDB entries from 2025-07-16

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