Macromolecule Annotations for the Entities in PDB 1OGY

Domain Annotation: SCOP Classification SCOP Database (version: 1.75) Homepage

Chains Domain Info Class Fold Superfamily Family Domain Species
A682-801 d1ogya1 All beta proteins Double psi beta-barrel ADC-like Formate dehydrogenase/DMSO reductase, C-terminal domain Periplasmic nitrate reductase alpha chain, NapA Rhodobacter sphaeroides [TaxId: 1063]
A12-681 d1ogya2 Alpha and beta proteins (a/b) Formate dehydrogenase/DMSO reductase, domains 1- 3 Formate dehydrogenase/DMSO reductase, domains 1- 3 Formate dehydrogenase/DMSO reductase, domains 1- 3 Periplasmic nitrate reductase alpha chain Rhodobacter sphaeroides [TaxId: 1063]
B d1ogyb_ All alpha proteins Multiheme cytochromes Multiheme cytochromes Di-heme elbow motif Periplasmic nitrate reductase subunit NapB Rhodobacter sphaeroides [TaxId: 1063]
C682-801 d1ogyc1 All beta proteins Double psi beta-barrel ADC-like Formate dehydrogenase/DMSO reductase, C-terminal domain Periplasmic nitrate reductase alpha chain, NapA Rhodobacter sphaeroides [TaxId: 1063]
C12-681 d1ogyc2 Alpha and beta proteins (a/b) Formate dehydrogenase/DMSO reductase, domains 1- 3 Formate dehydrogenase/DMSO reductase, domains 1- 3 Formate dehydrogenase/DMSO reductase, domains 1- 3 Periplasmic nitrate reductase alpha chain Rhodobacter sphaeroides [TaxId: 1063]
D d1ogyd_ All alpha proteins Multiheme cytochromes Multiheme cytochromes Di-heme elbow motif Periplasmic nitrate reductase subunit NapB Rhodobacter sphaeroides [TaxId: 1063]
E682-801 d1ogye1 All beta proteins Double psi beta-barrel ADC-like Formate dehydrogenase/DMSO reductase, C-terminal domain Periplasmic nitrate reductase alpha chain, NapA Rhodobacter sphaeroides [TaxId: 1063]
E12-681 d1ogye2 Alpha and beta proteins (a/b) Formate dehydrogenase/DMSO reductase, domains 1- 3 Formate dehydrogenase/DMSO reductase, domains 1- 3 Formate dehydrogenase/DMSO reductase, domains 1- 3 Periplasmic nitrate reductase alpha chain Rhodobacter sphaeroides [TaxId: 1063]
F d1ogyf_ All alpha proteins Multiheme cytochromes Multiheme cytochromes Di-heme elbow motif Periplasmic nitrate reductase subunit NapB Rhodobacter sphaeroides [TaxId: 1063]
G682-801 d1ogyg1 All beta proteins Double psi beta-barrel ADC-like Formate dehydrogenase/DMSO reductase, C-terminal domain Periplasmic nitrate reductase alpha chain, NapA Rhodobacter sphaeroides [TaxId: 1063]
G12-681 d1ogyg2 Alpha and beta proteins (a/b) Formate dehydrogenase/DMSO reductase, domains 1- 3 Formate dehydrogenase/DMSO reductase, domains 1- 3 Formate dehydrogenase/DMSO reductase, domains 1- 3 Periplasmic nitrate reductase alpha chain Rhodobacter sphaeroides [TaxId: 1063]
H d1ogyh_ All alpha proteins Multiheme cytochromes Multiheme cytochromes Di-heme elbow motif Periplasmic nitrate reductase subunit NapB Rhodobacter sphaeroides [TaxId: 1063]
I682-801 d1ogyi1 All beta proteins Double psi beta-barrel ADC-like Formate dehydrogenase/DMSO reductase, C-terminal domain Periplasmic nitrate reductase alpha chain, NapA Rhodobacter sphaeroides [TaxId: 1063]
I12-681 d1ogyi2 Alpha and beta proteins (a/b) Formate dehydrogenase/DMSO reductase, domains 1- 3 Formate dehydrogenase/DMSO reductase, domains 1- 3 Formate dehydrogenase/DMSO reductase, domains 1- 3 Periplasmic nitrate reductase alpha chain Rhodobacter sphaeroides [TaxId: 1063]
J d1ogyj_ All alpha proteins Multiheme cytochromes Multiheme cytochromes Di-heme elbow motif Periplasmic nitrate reductase subunit NapB Rhodobacter sphaeroides [TaxId: 1063]
K682-801 d1ogyk1 All beta proteins Double psi beta-barrel ADC-like Formate dehydrogenase/DMSO reductase, C-terminal domain Periplasmic nitrate reductase alpha chain, NapA Rhodobacter sphaeroides [TaxId: 1063]
K12-681 d1ogyk2 Alpha and beta proteins (a/b) Formate dehydrogenase/DMSO reductase, domains 1- 3 Formate dehydrogenase/DMSO reductase, domains 1- 3 Formate dehydrogenase/DMSO reductase, domains 1- 3 Periplasmic nitrate reductase alpha chain Rhodobacter sphaeroides [TaxId: 1063]
L d1ogyl_ All alpha proteins Multiheme cytochromes Multiheme cytochromes Di-heme elbow motif Periplasmic nitrate reductase subunit NapB Rhodobacter sphaeroides [TaxId: 1063]
M682-801 d1ogym1 All beta proteins Double psi beta-barrel ADC-like Formate dehydrogenase/DMSO reductase, C-terminal domain Periplasmic nitrate reductase alpha chain, NapA Rhodobacter sphaeroides [TaxId: 1063]
M12-681 d1ogym2 Alpha and beta proteins (a/b) Formate dehydrogenase/DMSO reductase, domains 1- 3 Formate dehydrogenase/DMSO reductase, domains 1- 3 Formate dehydrogenase/DMSO reductase, domains 1- 3 Periplasmic nitrate reductase alpha chain Rhodobacter sphaeroides [TaxId: 1063]
N d1ogyn_ All alpha proteins Multiheme cytochromes Multiheme cytochromes Di-heme elbow motif Periplasmic nitrate reductase subunit NapB Rhodobacter sphaeroides [TaxId: 1063]
O682-801 d1ogyo1 All beta proteins Double psi beta-barrel ADC-like Formate dehydrogenase/DMSO reductase, C-terminal domain Periplasmic nitrate reductase alpha chain, NapA Rhodobacter sphaeroides [TaxId: 1063]
O12-681 d1ogyo2 Alpha and beta proteins (a/b) Formate dehydrogenase/DMSO reductase, domains 1- 3 Formate dehydrogenase/DMSO reductase, domains 1- 3 Formate dehydrogenase/DMSO reductase, domains 1- 3 Periplasmic nitrate reductase alpha chain Rhodobacter sphaeroides [TaxId: 1063]
P d1ogyp_ All alpha proteins Multiheme cytochromes Multiheme cytochromes Di-heme elbow motif Periplasmic nitrate reductase subunit NapB Rhodobacter sphaeroides [TaxId: 1063]

Domain Annotation: CATH CATH Database (version 4.0.0) Homepage

Chains Domain Class Architecture Topology Homology
A2 1ogyA02 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold
A3 1ogyA03 Alpha Beta 3-Layer(aba) Sandwich Dimethylsulfoxide Reductase; domain 2 Dimethylsulfoxide Reductase, domain 2
A4 1ogyA04 Mainly Beta Beta Barrel Barwin-like endoglucanases
C2 1ogyC02 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold
C3 1ogyC03 Alpha Beta 3-Layer(aba) Sandwich Dimethylsulfoxide Reductase; domain 2 Dimethylsulfoxide Reductase, domain 2
C4 1ogyC04 Mainly Beta Beta Barrel Barwin-like endoglucanases
E2 1ogyE02 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold
E3 1ogyE03 Alpha Beta 3-Layer(aba) Sandwich Dimethylsulfoxide Reductase; domain 2 Dimethylsulfoxide Reductase, domain 2
E4 1ogyE04 Mainly Beta Beta Barrel Barwin-like endoglucanases
G2 1ogyG02 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold
G3 1ogyG03 Alpha Beta 3-Layer(aba) Sandwich Dimethylsulfoxide Reductase; domain 2 Dimethylsulfoxide Reductase, domain 2
G4 1ogyG04 Mainly Beta Beta Barrel Barwin-like endoglucanases
I2 1ogyI02 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold
I3 1ogyI03 Alpha Beta 3-Layer(aba) Sandwich Dimethylsulfoxide Reductase; domain 2 Dimethylsulfoxide Reductase, domain 2
I4 1ogyI04 Mainly Beta Beta Barrel Barwin-like endoglucanases
K2 1ogyK02 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold
K3 1ogyK03 Alpha Beta 3-Layer(aba) Sandwich Dimethylsulfoxide Reductase; domain 2 Dimethylsulfoxide Reductase, domain 2
K4 1ogyK04 Mainly Beta Beta Barrel Barwin-like endoglucanases
M2 1ogyM02 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold
M3 1ogyM03 Alpha Beta 3-Layer(aba) Sandwich Dimethylsulfoxide Reductase; domain 2 Dimethylsulfoxide Reductase, domain 2
M4 1ogyM04 Mainly Beta Beta Barrel Barwin-like endoglucanases
O2 1ogyO02 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold
O3 1ogyO03 Alpha Beta 3-Layer(aba) Sandwich Dimethylsulfoxide Reductase; domain 2 Dimethylsulfoxide Reductase, domain 2
O4 1ogyO04 Mainly Beta Beta Barrel Barwin-like endoglucanases

Protein Family Annotation Pfam Database Homepage

Chains Pfam Accession Pfam Identifier Pfam Description Type Source
B PF03892 NapB Nitrate reductase cytochrome c-type subunit (NapB) Family
A PF00384 Molybdopterin Molybdopterin oxidoreductase Family
A PF01568 Molydop_binding Molydopterin dinucleotide binding domain Domain This domain is found in various molybdopterin - containing oxidoreductases and tungsten formylmethanofuran dehydrogenase subunit d (FwdD) and molybdenum formylmethanofuran dehydrogenase subunit (FmdD); where the domain constitutes almost the entire subunit. The formylmethanofuran dehydrogenase catalyses the first step in methane formation from CO2 in methanogenic archaea and has a molybdopterin dinucleotide cofactor [1]. This domain corresponds to the C-terminal domain IV in dimethyl sulfoxide (DMSO)reductase which interacts with the 2-amino pyrimidone ring of both molybdopterin guanine dinucleotide molecules [2]. PFAM PF01568
A PF04879 Molybdop_Fe4S4 Molybdopterin oxidoreductase Fe4S4 domain Domain This domain is found in formate dehydrogenase H for which the structure is known. The first domain (residues 1 to 60, 448 to 476, and 499 to 540), comprising two small antiparallel sheets and four helices, coordinates the Fe4S4 cluster just below the protein surface [1]. PFAM PF04879

Gene Product Annotation Gene Ontology Consortium Homepage

Protein Modification Annotation

Type PDB Residue Nr. Description