Ribonucleotide reductase 3D structures

From Proteopedia

3D Structures of Ribonucleotide reductase

Updated on 08-August-2024

Class Ia ribonucleotide reductase

Ribonucleotide reductase large subunit R1

1zyz, 1zzd, 2cvs, 2cvt, 2cvu, 2cvv, 2cvw, 2cvx, 2cvy - yRNR R1 – yeast

1rlr - EcRNR R1 – Escherichia coli

1mrr - EcRNR R1 + Mn

5r1r, 6r1r, 7r1r, 1r1r – EcRNR R1 (mutant) + R2

Ribonucleotide reductase large subunit complex

3hnc – hRNR M1 + TTP – human

3hnd – hRNR M1 + GDP + TTP

3hne, 3hnf – hRNR M1 + ATP + TTP

2wgh, 5d1y - hRNR M1 + ATP + Mg

6aui - hRNR M1 + ATP + CDP

5tus, 4x3v, 6l3r, 6l7l, 6lkm - hRNR M1 + inhibitor + TTP

3paw - yRNR R1 + ATP

3k8t - yRNR R1 + ADP analog

3s87 - yRNR R1 + ADP + GTP

3s8a - yRNR R1 (mutant) + GTP

3tba - yRNR R1 (mutant) + GTP + ADP

3s8b - yRNR R1 + AMPPNP + CDP

3s8c, 3tb9 - yRNR R1 (mutant) + AMPPNP + CDP

2zlf, 2zlg - yRNR R1 + peptide

2eud - yRNR R1 + ligand

3rsr – yRNR R1 + inhibitor

1qfn - EcRNR R1 + glutaredoxin 1

7agj - AaRNR R1 + ATP – Aquifex aeolicus

RNR small subunit R2

3hf1, 2vux, 2uw2, 4djn, 3olj – hRNR M2

3vpm, 3vpn, 3vpo – hRNR M2 (mutant)

1w68, 1h0n, 1h0o, 1xsm – mRNR R2 – mouse

1smq, 1sms – yRNR 2

1jk0 – yRNR Y2+Y4

2xof, 1av8, 1rib – EcRNR R2 + Fe2O

2alx, 1jqc, 1jpr - EcRNR R2 + Mn

1piy, 1r65, 1mxr, 1xik, 7ai8, 7ai9, 7bet - EcRNR R2 + Fe

1piz, 1pj0, 1pj1, 1pim, 1piu, 1biq, 1pfr - EcRNR R2 (mutant) + Fe

1yfd, 2av8 - EcRNR R2 (mutant) + Fe2O

1pm2 - EcRNR R2 (mutant) + Mn

2p1i – RNR R2 – Plasmodium yoelii

2o1z - RNR R2 – Plasmodium vivax

4d8f, 4d8g, 4m1i - CtRNR R2 + Fe + Mn

1syy - CtRNR R2 + Fe + Pb– Chlamydia trachomatis

2ani - CtRNR R2 (mutant) + Fe + Pb

4m1h - CtRNR R2

1uzr – MtRNR R2 – Mycobacterium tuberculosis

2rcc – RNR – Bacillus halodurans

4n83 - SsRNR + Mn

4hr5 - GkRNR – Geobacillus kaustophilus

5omj, 5omk - GkRNR + Fe

4hr0, 4hr4 - GkRNR + Fe + Mn

6f6c, 6f6e, 6f6f, 6f6g, 6f6h, 6f6k, 6qjv, 6qk0, 6qk1, 6qk2 - GkRNR (mutant) + Fe + Mn

6cwo, 6cwq - FjRNR + Mn – Flavobacterium johnsoniae

6gp2, 6gp3 - RNR R2 – Mesoplasma florum

7aik, 7ail, 7q39, 7q3c - AaRNR R2

6y2n - RNR R2 – Saccharopolyspora erythraea

6ebz, 6ebz - AuRNR R2 – Aerococcus urinae

6qrz - RNR R2 – Sulfolobus acidocaldarius

6zjk - RNR R2 – Clostridium botulinum

Ribonucleotide reductase small subunit complex

1w69 – mRNR R2 + acetate

1rsr, 1rsv - EcRNR R2 (mutant) + Fe + N3

1rnr – EcRNR R2 (mutant) + Fe + dopa

5ci4 – EcRNR R2 (mutant) + Fe2O

5ci3, 5ci0, 5ci1, 5ci2 – EcRNR R2 (mutant) + fluoro-tyrosine + Fe₂O

6cwp – FjRNR + Mn + peptide

4xbw – GkRNR + Mn

6i94 – GkRNR (mutant) + Mn

5dco, 4xb9, 4xbv – GkRNR + Fe

6i93 – GkRNR (mutant) + Fe

5dcr, 5dcs – GkRNR + Mn + Fe

6i90, 6i92, 6i95, 6f65, 6f6b, 6f6l, 6f6m, 5ekb, 6qjv, 6qk0, 6qk1, 6qk2 – GkRNR (mutant) + Mn + Fe

4ac8 – MtRNR + Mn + Fe

Ribonucleotide reductase small+large subunit

1r1r, 5r1r, 6r1r, 7r1r, 1r1r – EcRNR R1 (mutant) + R2

3uus - EcRNR R1+ R2 + Fe + ATP

4erm - EcRNR R1+ R2 + Fe2O + ATP + ADP

4erp - EcRNR R1+ R2 + Fe2O + ATP

2xak, 2xap, 2xo4, 2xo5 - EcRNR R1 modified+ R2 peptide

2xav, 2xaw, 2xax, 2xay, 2xaz, 2x0x - EcRNR R1 (mutant) modified + R2 peptide

5cns, 5cnt, 5cnv, 5cnu - EcRNR R1 + R2 + Fe2O + 2 nucleotides

2r1r - EcRNR R1 + R2 + TTP

3r1r - EcRNR R1 + R2 + AMPPNP

6w4x - EcRNR R1 + R2 + GDP + TTP – Cryo EM

4r1r - EcRNR R1 + R2 + GDP + TTP

2bq1 - StRNR R1+ R2

5im3 - RNR + dATP – Pseudomonas aeruginosa

7mdi - RNR R1 + R2 + CDP + DTP – Neisseria gonorrhoea - Cryo EM

Class Ib RNR ; NrdE – large subunit; NrdF – small subunit; NrdI – FMN containing flavoprotein

6cgm - BaRNR NrdE – Bacillus subtilis

6qo5, 6qo7, 6qo8, 6qo9, 6qob, 6tqv, 6tqw, 6tqx - BaRNR NrdF

6tqy, 6tqz - BaRNR NrdF (mutant)

4dr0 - BaRNR NrdF + Mn

6myx - BaRNR NrdE + DTP – Cryo EM

6mv9 - BaRNR NrdE + TTP + ADP

6mt9, 6mve - BaRNR NrdE + TTP + ADP + ATP

6mw3 - BaRNR NrdE + NrdF + DTP – Cryo EM

6cgn, 6cgl - BaRNR NrdE + AMP derivative

1pem - StRNR NrdE – Salmonella typhimurium

1peo, 1peq, 1peu - StRNR NrdE + nucleotide

2bq1 - StRNR NrdE + NrdF + Fe + GTP

1r2f - StRNR NrdF + Fe

2r2f - StRNR NrdF + Fe2O

4dr0 - BaRNR NrdF + Mn

4bmq, 4bmr, 4bmt - BcRNR NrdF + Fe – Bacillus cereus

4bmu - BcRNR NrdF + Mn

4bmo, 4bmp - BcRNR NrdF + NrdI + Fe + FMN

7z3d, 7z3e - BcRNR NrdF + NrdI + Mn + FMN

4m1f - EcRNR NrdF

3n37 - EcRNR NrdF + Mn

3n38 - EcRNR NrdF + Fe

3n39, 3n3a - EcRNR NrdF + NrdI + Mn + FMN

3n3b - EcRNR NrdF + NrdI + Mn + FMN + Fe2O

4n82 – SsRNR + FMN – Streptococcus sanguinis

4n83 - SsRNR NrdF + Mn

3mjo - CaRNR NrdF + Mn - Corynebacterium ammoniagenes

1kgn, 1kgo, 1kgp, 1oqu, 3dhz - CaRNR NrdF + Fe

Class Id RNR or ribonucleotide-diphosphate reductase; NrdB – small subunit

6sf4, 6sf5 - RNR β subunit – Leeuwenhoekiella blandensis

6cwo, 6cwq - FjRNR b subunit 1-324 + Mn – Flavobacterium johnsoniae

8dq4, 8dq5 - FjRNR b subunit (mutant) + Mn

6dqw - FjRNR a subunit 1-565

6dqx - RNR a subunit – Actinobacillus ureae

8dq3 - RNR b subunit + Mn – Aggregatibacter actinomycetemcomitans

Class Ie RNR

6ebo - AuRNR beta subunit - Aerococcus urinae

7mms, 7mmt, 7mmu, 7mmv, 7mmw - AuRNR beta subunit + Cu

6ebp - AuRNR beta subunit + L-Dopa

6ebz - AuRNR beta subunit + L-Dopa + SCN

6ebq - AuRNR NrdI + FMN

7mmp, 7mmq - AuRNR + NrdI + FMN

7mmr - AuRNR + NrdI + FMN + Cu

6dqx - RNR α subunit – Actinobacillus ureae

Class II ribonucleotide reductase

1xjf, 4col – TmRNR + DATP – Thermotoga maritima

4coi, 4com, 4con – TmRNR

1xjg, 1xjk, 1xje, 1xjn, 4coj - TmRNR + 2 nucleotides

1xjj - TmRNR + GTP

1xjm - TmRNR + TTP

3o0n - TmRNR + TTP + Co + Mg + deoxyadenosine + B12

3o0o - TmRNR + TTP + GDP + Mg + deoxyadenosine + B12

3o0q - TmRNR + TTP + GDP + Mg + adenosine

1l1l – RNR (mutant) – Lactobacillus leichmannii

Class III ribonucleotide reductase

1h78, 1h79, 1h7a, 1hk8 – T4RNR (mutant) + nucleotide triphosphate – bacteriophage T4

1h7b – T4RNR (mutant)

4u3e – TmRNR large subunit

Vitamin B12-dependent RNR

7b9p, 7b9q – RNR + DTP – Rhodobacter sphaeroides

Anaerobic ribonucleotide-triphosphate reductase

8p23, 8p27, 8p28, 8p2c, 8p2d, 8p2s, 8p39 – ARNR + DTP – Segatella copri - Cryo EM

RNR

7urg – RNR + TTP – Synechococcus phage – Cryo EM