The crystal structure of the large ribosomal subunit of Staphylococcus aureus in complex with lincomycin
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
---|---|---|---|---|---|
I [auth H] | SCOP2B Superfamily | 50S Ribosomal protein L14-like | 8093892 | 3000433 | SCOP2B (2022-06-29) |
H [auth G] | SCOP2B Superfamily | Ribosomal protein L13 | 8066059 | 3001134 | SCOP2B (2022-06-29) |
E [auth C] | SCOP2B Superfamily | Ribosomal protein L4 | 8094174 | 3001146 | SCOP2B (2022-06-29) |
D [auth B] | SCOP2B Superfamily | Translational proteins | 8089152 | 3000811 | SCOP2B (2022-06-29) |
AA [auth 3] | SCOP2B Superfamily | L35p-like | 8083334 | 3000790 | SCOP2B (2022-06-29) |
X [auth W] | SCOP2B Superfamily | Ribosomal protein L30p/L7e | 8076281 | 3001378 | SCOP2B (2022-06-29) |
W [auth V] | SCOP2B Superfamily | Ribosomal protein L29 (L29p) | 8094170 | 3000713 | SCOP2B (2022-06-29) |
U [auth T] | SCOP2B Superfamily | Ribosomal L27 protein-like | 8075030 | 3000539 | SCOP2B (2022-06-29) |
T [auth S] | SCOP2B Superfamily | Ribosomal protein L25-like | 8082277 | 3001161 | SCOP2B (2022-06-29) |
S [auth R] | SCOP2B Superfamily | Translation proteins SH3-like KOW motif containing domain | 8082503 | 3000334 | SCOP2B (2022-06-29) |
R [auth Q] | SCOP2B Superfamily | Ribosomal proteins S24e, L23 and L15e | 8086046 | 3000210 | SCOP2B (2022-06-29) |
Q [auth P] | SCOP2B Superfamily | Ribosomal protein L22 | 8076726 | 3001078 | SCOP2B (2022-06-29) |
P [auth O] | SCOP2B Superfamily | l21p-like | 8094148 | 3002005 | SCOP2B (2022-06-29) |
O [auth N] | SCOP2B Superfamily | Ribosomal protein L20 | 8094941 | 3000563 | SCOP2B (2022-06-29) |
N [auth M] | SCOP2B Superfamily | Translation proteins SH3-like KOW motif containing domain | 8082423 | 3000334 | SCOP2B (2022-06-29) |
L [auth K] | SCOP2B Superfamily | Prokaryotic ribosomal protein L17 | 8089022 | 3000995 | SCOP2B (2022-06-29) |
K [auth J] | SCOP2B Superfamily | Ribosomal protein L16p/L10e | 8076041 | 3000884 | SCOP2B (2022-06-29) |
J [auth I] | SCOP2B Superfamily | Ribosomal proteins L15p and L18e | 8070555 | 3001045 | SCOP2B (2022-06-29) |
Domain Annotation: ECOD Classification ECOD Database Homepage
Chains | Family Name | Domain Identifier | Architecture | Possible Homology | Homology | Topology | Family | Provenance Source (Version) |
---|---|---|---|---|---|---|---|---|
I [auth H] | Ribosomal_L14 | e5hkvH1 | A: beta barrels | X: Ribosomal protein L14-like | H: Ribosomal protein L14-related (From Topology) | T: Ribosomal protein L14-related | F: Ribosomal_L14 | ECOD (1.6) |
H [auth G] | Ribosomal_L13 | e5hkvG1 | A: a/b three-layered sandwiches | X: Ribosomal protein L13/L15p/L18e/L32e | H: Ribosomal protein L13 and L16-A (From Topology) | T: Ribosomal protein L13 and L16-A | F: Ribosomal_L13 | ECOD (1.6) |
G [auth E] | Ribosomal_L6 | e5hkvE1 | A: a+b two layers | X: Ribosomal protein L6 (From Topology) | H: Ribosomal protein L6 (From Topology) | T: Ribosomal protein L6 | F: Ribosomal_L6 | ECOD (1.6) |
G [auth E] | Ribosomal_L6_1 | e5hkvE2 | A: a+b two layers | X: Ribosomal protein L6 (From Topology) | H: Ribosomal protein L6 (From Topology) | T: Ribosomal protein L6 | F: Ribosomal_L6_1 | ECOD (1.6) |
F [auth D] | Ribosomal_L5_C | e5hkvD1 | A: a+b two layers | X: Ribosomal protein L5 (From Topology) | H: Ribosomal protein L5 (From Topology) | T: Ribosomal protein L5 | F: Ribosomal_L5_C | ECOD (1.6) |
E [auth C] | Ribosomal_L4 | e5hkvC1 | A: a/b three-layered sandwiches | X: Ribosomal protein L4 (From Topology) | H: Ribosomal protein L4 (From Topology) | T: Ribosomal protein L4 | F: Ribosomal_L4 | ECOD (1.6) |
D [auth B] | Ribosomal_L3 | e5hkvB1 | A: beta barrels | X: cradle loop barrel | H: RIFT-related | T: Alanine racemase-C | F: Ribosomal_L3 | ECOD (1.6) |
C [auth A] | Ribosomal_L2_1 | e5hkvA2 | A: beta barrels | X: OB-fold | H: Nucleic acid-binding proteins (From Topology) | T: Nucleic acid-binding proteins | F: Ribosomal_L2_1 | ECOD (1.6) |
C [auth A] | Ribosomal_L2_C_2 | e5hkvA1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: Ribosomal_L2_C_2 | ECOD (1.6) |
AA [auth 3] | Ribosomal_L35p | e5hkv31 | A: a+b two layers | X: Ribosomal protein L35p (From Topology) | H: Ribosomal protein L35p (From Topology) | T: Ribosomal protein L35p | F: Ribosomal_L35p | ECOD (1.6) |
Z [auth 2] | Ribosomal_L34 | e5hkv21 | A: extended segments | X: 50S ribosomal protein L34 (From Topology) | H: 50S ribosomal protein L34 (From Topology) | T: 50S ribosomal protein L34 | F: Ribosomal_L34 | ECOD (1.6) |
Y [auth Z] | Ribosomal_L32p | e5hkvZ1 | A: few secondary structure elements | X: Rubredoxin-like | H: Rubredoxin-related | T: Rubredoxin-related | F: Ribosomal_L32p | ECOD (1.6) |
X [auth W] | Ribosomal_L30 | e5hkvW1 | A: a+b two layers | X: Ribosomal protein L30p/L7e (From Topology) | H: Ribosomal protein L30p/L7e (From Topology) | T: Ribosomal protein L30p/L7e | F: Ribosomal_L30 | ECOD (1.6) |
W [auth V] | Ribosomal_L29 | e5hkvV1 | A: alpha bundles | X: Long alpha-hairpin | H: Ribosomal protein L29 (L29p) (From Topology) | T: Ribosomal protein L29 (L29p) | F: Ribosomal_L29 | ECOD (1.6) |
V [auth U] | Ribosomal_L28 | e5hkvU1 | A: few secondary structure elements | X: Ribosomal protein bL28-related (From Homology) | H: Ribosomal protein bL28-related | T: Ribosomal protein L28 | F: Ribosomal_L28 | ECOD (1.6) |
U [auth T] | Ribosomal_L27 | e5hkvT1 | A: a+b complex topology | X: alpha/beta-Hammerhead/Barrel-sandwich hybrid | H: alpha/beta-Hammerhead/Barrel-sandwich hybrid | T: Ribosomal L27 protein | F: Ribosomal_L27 | ECOD (1.6) |
T [auth S] | Ribosomal_L25p | e5hkvS2 | A: beta barrels | X: Ribosomal protein L25-like | H: Ribosomal protein L25-like (From Topology) | T: Ribosomal protein L25-like | F: Ribosomal_L25p | ECOD (1.6) |
T [auth S] | Ribosomal_TL5_C_1 | e5hkvS1 | A: a+b complex topology | X: Ribosomal protein TL5/L25 C-terminal domain-like | H: Ribosomal protein TL5/L25 C-terminal domain-related (From Topology) | T: Ribosomal protein TL5/L25 C-terminal domain-related | F: Ribosomal_TL5_C_1 | ECOD (1.6) |
S [auth R] | ribosomal_L24_1 | e5hkvR1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: ribosomal_L24_1 | ECOD (1.6) |
R [auth Q] | Ribosomal_L23_2 | e5hkvQ1 | A: a+b two layers | X: Alpha-beta plaits | H: Ribosomal proteins S24e, L23 and L15e (From Topology) | T: Ribosomal proteins S24e, L23 and L15e | F: Ribosomal_L23_2 | ECOD (1.6) |
Q [auth P] | Ribosomal_L22 | e5hkvP1 | A: a+b two layers | X: Enolase-N/ribosomal protein | H: Ribosomal protein L22 (From Topology) | T: Ribosomal protein L22 | F: Ribosomal_L22 | ECOD (1.6) |
P [auth O] | Ribosomal_L21p | e5hkvO1 | A: beta barrels | X: Ribosomal protein L21p (From Topology) | H: Ribosomal protein L21p (From Topology) | T: Ribosomal protein L21p | F: Ribosomal_L21p | ECOD (1.6) |
O [auth N] | Ribosomal_L20 | e5hkvN1 | A: alpha arrays | X: PABP domain-like | H: Ribosomal protein L20 (From Topology) | T: Ribosomal protein L20 | F: Ribosomal_L20 | ECOD (1.6) |
N [auth M] | Ribosomal_L19 | e5hkvM1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: Ribosomal_L19 | ECOD (1.6) |
M [auth L] | Ribosomal_L18p | e5hkvL1 | A: mixed a+b and a/b | X: Ribonuclease H-like | H: Ribonuclease H-like (From Topology) | T: Ribonuclease H-like | F: Ribosomal_L18p | ECOD (1.6) |
L [auth K] | Ribosomal_L17_1 | e5hkvK1 | A: a+b two layers | X: Enolase-N/ribosomal protein | H: Prokaryotic ribosomal protein L17 (From Topology) | T: Prokaryotic ribosomal protein L17 | F: Ribosomal_L17_1 | ECOD (1.6) |
K [auth J] | Ribosomal_L16 | e5hkvJ1 | A: a+b complex topology | X: alpha/beta-Hammerhead/Barrel-sandwich hybrid | H: alpha/beta-Hammerhead/Barrel-sandwich hybrid | T: Ribosomal protein L10e | F: Ribosomal_L16 | ECOD (1.6) |
J [auth I] | Ribosomal_L27A | e5hkvI1 | A: a/b three-layered sandwiches | X: Ribosomal protein L13/L15p/L18e/L32e | H: Ribosomal proteins L15p and L18e (From Topology) | T: Ribosomal proteins L15p and L18e | F: Ribosomal_L27A | ECOD (1.6) |
Domain Annotation: CATH CATH Database Homepage
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
I [auth H] | PF00238 | Ribosomal protein L14p/L23e (Ribosomal_L14) | Ribosomal protein L14p/L23e | Domain | |
H [auth G] | PF00572 | Ribosomal protein L13 (Ribosomal_L13) | Ribosomal protein L13 | - | Family |
G [auth E] | PF00347 | Ribosomal protein L6 (Ribosomal_L6) | Ribosomal protein L6 | Domain | |
F [auth D] | PF00281 | Ribosomal protein L5 (Ribosomal_L5) | Ribosomal protein L5 | Domain | |
F [auth D] | PF00673 | ribosomal L5P family C-terminus (Ribosomal_L5_C) | ribosomal L5P family C-terminus | This region is found associated with Pfam:PF00281. | Domain |
E [auth C] | PF00573 | Ribosomal protein L4/L1 family (Ribosomal_L4) | Ribosomal protein L4/L1 family | - | Family |
D [auth B] | PF00297 | Ribosomal protein L3 (Ribosomal_L3) | Ribosomal protein L3 | - | Family |
C [auth A] | PF03947 | Ribosomal Proteins L2, C-terminal domain (Ribosomal_L2_C) | Ribosomal Proteins L2, C-terminal domain | Domain | |
C [auth A] | PF00181 | Ribosomal Proteins L2, RNA binding N-terminal domain (Ribosomal_L2_N) | Ribosomal Proteins L2, RNA binding N-terminal domain | Domain | |
AA [auth 3] | PF01632 | Ribosomal protein L35 (Ribosomal_L35p) | Ribosomal protein L35 | - | Family |
Z [auth 2] | PF00468 | Ribosomal protein L34 (Ribosomal_L34) | Ribosomal protein L34 | - | Family |
Y [auth Z] | PF01783 | Ribosomal L32p protein family (Ribosomal_L32p) | Ribosomal L32p protein family | - | Family |
X [auth W] | PF00327 | Ribosomal protein L30p/L7e (Ribosomal_L30) | Ribosomal protein L30p/L7e | This family includes prokaryotic L30 and eukaryotic L7. | Domain |
W [auth V] | PF00831 | Ribosomal L29 protein (Ribosomal_L29) | Ribosomal L29 protein | - | Family |
T [auth S] | PF14693 | Ribosomal protein TL5, C-terminal domain (Ribosomal_TL5_C) | Ribosomal protein TL5, C-terminal domain | This family contains the C-terminal domain of ribosomal protein TL5. The N-terminal domain, which binds to 5S rRNA, is contained in family Ribosomal_L25p, Pfam:PF01386. Full length (N- and C-terminal domain) homologues of TL5 are also known as CTC pr ... | Domain |
T [auth S] | PF01386 | Ribosomal L25p family (Ribosomal_L25p) | Ribosomal L25p family | Ribosomal protein L25 is an RNA binding protein, that binds 5S rRNA. This family includes Ctc from B. subtilis Swiss:P14194, which is induced by stress. | Domain |
S [auth R] | PF17136 | Large ribosomal subunit protein uL24, C-terminal domain (ribosomal_L24) | Large ribosomal subunit protein uL24, C-terminal domain | This entry describes the C-terminal domain in large ribosomal subunit protein uL24 (also known as RPL26). RPL26 is one of the proteins from the large ribosomal subunit. In their mature form, these proteins have 103 to 150 amino-acid residues. RPL26 m ... | Domain |
S [auth R] | PF00467 | KOW motif (KOW) | KOW motif | - | Family |
R [auth Q] | PF00276 | Ribosomal protein L23 (Ribosomal_L23) | Ribosomal protein L23 | - | Family |
Q [auth P] | PF00237 | Ribosomal protein L22p/L17e (Ribosomal_L22) | Ribosomal protein L22p/L17e | This family includes L22 from prokaryotes and chloroplasts and L17 from eukaryotes. | Domain |
P [auth O] | PF00829 | Ribosomal prokaryotic L21 protein (Ribosomal_L21p) | Ribosomal prokaryotic L21 protein | - | Family |
O [auth N] | PF00453 | Ribosomal protein L20 (Ribosomal_L20) | Ribosomal protein L20 | - | Family |
N [auth M] | PF01245 | Ribosomal protein L19 (Ribosomal_L19) | Ribosomal protein L19 | - | Family |
M [auth L] | PF00861 | Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast (Ribosomal_L18p) | Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast | - | Family |
L [auth K] | PF01196 | Ribosomal protein L17 (Ribosomal_L17) | Ribosomal protein L17 | - | Family |
K [auth J] | PF00252 | Ribosomal protein L16p/L10e (Ribosomal_L16) | Ribosomal protein L16p/L10e | Domain | |
J [auth I] | PF00828 | Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A (Ribosomal_L27A) | Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A | This family includes higher eukaryotic ribosomal 60S L27A, archaeal 50S L18e, prokaryotic 50S L15, fungal mitochondrial L10, plant L27A, mitochondrial L15 and chloroplast L18-3 proteins. | Domain |