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3DFR

CRYSTAL STRUCTURES OF ESCHERICHIA COLI AND LACTOBACILLUS CASEI DIHYDROFOLATE REDUCTASE REFINED AT 1.7 ANGSTROMS RESOLUTION. I. GENERAL FEATURES AND BINDING OF METHOTREXATE

Replaces:  1DFR
Functional Information from GO Data
ChainGOidnamespacecontents
A0004146molecular_functiondihydrofolate reductase activity
A0005829cellular_componentcytosol
A0006545biological_processglycine biosynthetic process
A0006730biological_processone-carbon metabolic process
A0016491molecular_functionoxidoreductase activity
A0031427biological_processresponse to methotrexate
A0046452biological_processdihydrofolate metabolic process
A0046654biological_processtetrahydrofolate biosynthetic process
A0046655biological_processfolic acid metabolic process
A0046677biological_processresponse to antibiotic
A0050661molecular_functionNADP binding
Functional Information from PDB Data
site_idAC1
Number of Residues34
DetailsBINDING SITE FOR RESIDUE NDP A 163
ChainResidue
AHOH326
AHOH373
AHOH401
AHOH439
AHOH579
ATRP5
AALA6
AILE13
AGLY14
ALYS15
AGLY17
AHIS18
ALEU19
AGLY42
AARG43
AARG44
ATHR45
ALEU62
ATHR63
AHIS64
AGLN65
AHIS77
AALA97
AGLY99
AALA100
AGLN101
AILE102
AMTX164
AHOH208
AHOH276
AHOH279
AHOH301
AHOH302
AHOH318

site_idAC2
Number of Residues21
DetailsBINDING SITE FOR RESIDUE MTX A 164
ChainResidue
ALEU4
ATRP5
ALEU19
AASP26
ALEU27
AHIS28
APHE30
AARG31
ASER48
APHE49
APRO50
AARG57
AALA97
ATHR116
ANDP163
AHOH322
AHOH329
AHOH331
AHOH559
AHOH606
AHOH621

site_idMAB
Number of Residues5
DetailsRESIDUES INTERACTING WITH THE P-AMINOBENZOYL OF THE METHOTREXATE INHIBITOR
ChainResidue
ALEU27
APHE30
APHE49
APRO50
ALEU54

site_idMGL
Number of Residues6
DetailsRESIDUES INTERACTING WITH THE GLUTAMATE OF THE METHOTREXATE INHIBITOR
ChainResidue
ALEU27
AHIS28
APHE30
AARG31
ALEU54
AARG57

site_idMNM
Number of Residues2
DetailsRESIDUES INTERACTING WITH THE N(10) METHYL OF THE METHOTREXATE INHIBITOR
ChainResidue
ALEU19
ASER48

site_idMPT
Number of Residues14
DetailsRESIDUES INTERACTING WITH THE PTERIDINE of THE METHOTREXATE INHIBITOR
ChainResidue
ALEU4
ATRP5
AALA6
ALEU19
ATRP21
AASP26
ALEU27
APHE30
AALA97
ATHR116
ANDP163
AHOH201
AHOH217
AHOH253

site_idNAR
Number of Residues9
DetailsRESIDUES INTERACTING WITH THE ADENINE MONONUCLEOTIDE RIBOSE OF THE NADPH COFACTOR
ChainResidue
AARG43
AARG44
ATHR63
AHIS64
AGLN65
AGLN101
AILE102
AHOH401
AGLY42

site_idNDN
Number of Residues8
DetailsRESIDUES INTERACTING WITH THE ADENINE BASE OF THE NADPH COFACTOR
ChainResidue
ALEU62
ATHR63
AHIS64
AHIS77
AGLN101
AILE102
AHOH279
AHOH318

site_idNMR
Number of Residues7
DetailsRESIDUES INTERACTING WITH THE NICOTINAMIDE MONONUCLEOTIDE RIBOSE OF THE NADPH COFACTOR
ChainResidue
AILE13
AGLY14
AHIS18
ASER48
AGLY99
AHOH208
AHOH439

site_idNND
Number of Residues12
DetailsRESIDUES INTERACTING WITH THE NICOTINAMIDE BASE OF THE NADPH COFACTOR
ChainResidue
ATRP5
AALA6
AILE13
ALEU19
ATRP21
ATHR45
AALA97
AGLY98
AGLY99
APHE103
AMTX164
AHOH439

site_idNPP
Number of Residues7
DetailsRESIDUES INTERACTING WITH THE PYROPHOSPHATE OF THE NADPH COFACTOR
ChainResidue
AARG44
ATHR45
AGLY99
AGLN101
AILE102
ATHR126
AHOH301

Functional Information from PROSITE/UniProt
site_idPS00075
Number of Residues23
DetailsDHFR_1 Dihydrofolate reductase (DHFR) domain signature. LIGkdghLPWhlpd.DlhyFraqT
ChainResidueDetails
ALEU12-THR34

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues5
DetailsBINDING: BINDING => ECO:0000305|PubMed:6815179
ChainResidueDetails
ATRP5
ALEU27
AALA32
ATHR58
AARG117

site_idSWS_FT_FI2
Number of Residues6
DetailsBINDING: BINDING => ECO:0000269|PubMed:6815179
ChainResidueDetails
AALA6
AGLY14
AARG43
ATHR63
AALA80
AGLY98

site_idSWS_FT_FI3
Number of Residues1
DetailsSITE: May be important for enzyme function
ChainResidueDetails
AHIS22

Catalytic Information from CSA
site_idMCSA1
Number of Residues9
DetailsM-CSA 112
ChainResidueDetails
ATRP5steric role
APRO20enhance reactivity
AHIS22activator, hydrogen bond donor
ALEU27hydrogen bond acceptor, modifies pKa
AHIS28steric locator
AARG31steric locator
APRO55steric locator
AVAL95steric role
AARG117electrostatic stabiliser, hydrogen bond donor

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PDB entries from 2024-04-24

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