6I9R
Large subunit of the human mitochondrial ribosome in complex with Virginiamycin M and Quinupristin
This is a non-PDB format compatible entry.
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | 0 | 39S ribosomal protein L32, mitochondrial | polymer | 188 | 21437.8 | 1 | UniProt (Q9BYC8) Pfam (PF01783) In PDB | Homo sapiens (human) | MRP-L32,Mitochondrial large ribosomal subunit protein bL32m |
| 2 | 1 | 39S ribosomal protein L33, mitochondrial | polymer | 65 | 7635.2 | 1 | UniProt (O75394) Pfam (PF00471) In PDB | Homo sapiens (human) | MRP-L33,Mitochondrial large ribosomal subunit protein bL33m |
| 3 | 2 | 39S ribosomal protein L34, mitochondrial | polymer | 92 | 10183.9 | 1 | UniProt (Q9BQ48) Pfam (PF00468) In PDB | Homo sapiens (human) | MRP-L34,Mitochondrial large ribosomal subunit protein bL34m |
| 4 | 3 | 39S ribosomal protein L35, mitochondrial | polymer | 188 | 21558.5 | 1 | UniProt (Q9NZE8) Pfam (PF01632) In PDB | Homo sapiens (human) | MRP-L35,Mitochondrial large ribosomal subunit protein bL35m |
| 5 | 4 | 39S ribosomal protein L36, mitochondrial | polymer | 103 | 11809.3 | 1 | UniProt (Q9P0J6) Pfam (PF00444) In PDB | Homo sapiens (human) | MRP-L36,BRCA1-interacting protein 1,Mitochondrial large ribosomal subunit protein bL36m |
| 6 | 5 | 39S ribosomal protein L37, mitochondrial | polymer | 423 | 48183.3 | 1 | UniProt (Q9BZE1) Pfam (PF07147) In PDB | Homo sapiens (human) | MRP-L37,39S ribosomal protein L2,mitochondrial,MRP-L2,Mitochondrial large ribosomal subunit protein mL37 |
| 7 | 6 | 39S ribosomal protein L38, mitochondrial | polymer | 380 | 44659.4 | 1 | UniProt (Q96DV4) Pfam (PF01161) In PDB | Homo sapiens (human) | MRP-L38,Mitochondrial large ribosomal subunit protein mL38 |
| 8 | 7 | 39S ribosomal protein L39, mitochondrial | polymer | 338 | 38764.8 | 1 | UniProt (Q9NYK5) In PDB | Homo sapiens (human) | MRP-L39,39S ribosomal protein L5,mitochondrial,MRP-L5,Mitochondrial large ribosomal subunit protein mL39 |
| 9 | 8 | 39S ribosomal protein L40, mitochondrial | polymer | 206 | 24534.4 | 1 | UniProt (Q9NQ50) Pfam (PF09812) In PDB | Homo sapiens (human) | MRP-L40,Mitochondrial large ribosomal subunit protein mL40,Nuclear localization signal-containing protein deleted in velocardiofacial syndrome,Up-regulated in metastasis |
| 10 | 9 | 39S ribosomal protein L41, mitochondrial | polymer | 137 | 15404.7 | 1 | UniProt (Q8IXM3) Pfam (PF09809) In PDB | Homo sapiens (human) | MRP-L41,39S ribosomal protein L27 homolog,Bcl-2-interacting mitochondrial ribosomal protein L41,Cell proliferation-inducing gene 3 protein,MRP-L27 homolog,Mitochondrial large ribosomal subunit protein mL41 |
| 11 | A | 16S rRNA | polymer | 1557 | 499421.3 | 1 | GenBank (1391841121) | Homo sapiens (human) | |
| 12 | B | tRNA Val | polymer | 69 | 22022.1 | 1 | GenBank (1485738021) | Homo sapiens (human) | |
| 13 | D | 39S ribosomal protein L2, mitochondrial | polymer | 305 | 33355.9 | 1 | UniProt (Q5T653) Pfam (PF00181) Pfam (PF03947) In PDB | Homo sapiens (human) | MRP-L2,Mitochondrial large ribosomal subunit protein uL2m |
| 14 | E | 39S ribosomal protein L3, mitochondrial | polymer | 348 | 38689.6 | 1 | UniProt (P09001) Pfam (PF00297) In PDB | Homo sapiens (human) | MRP-L3,Mitochondrial large ribosomal subunit protein uL3m |
| 15 | F | 39S ribosomal protein L4, mitochondrial | polymer | 311 | 34970.2 | 1 | UniProt (Q9BYD3) Pfam (PF00573) In PDB | Homo sapiens (human) | MRP-L4,Mitochondrial large ribosomal subunit protein uL4m |
| 16 | H | 39S ribosomal protein L9, mitochondrial | polymer | 267 | 30296.4 | 1 | UniProt (Q9BYD2) Pfam (PF01281) Pfam (PF22078) In PDB | Homo sapiens (human) | MRP-L9,Mitochondrial large ribosomal subunit protein bL9m |
| 17 | I | 39S ribosomal protein L10, mitochondrial | polymer | 261 | 29322.5 | 1 | UniProt (Q7Z7H8) Pfam (PF00466) In PDB | Homo sapiens (human) | MRP-L10,39S ribosomal protein L8,mitochondrial,MRP-L8,Mitochondrial large ribosomal subunit protein uL10m |
| 18 | J | 39S ribosomal protein L11, mitochondrial | polymer | 192 | 20716.2 | 1 | UniProt (Q9Y3B7) Pfam (PF03946) Pfam (PF00298) In PDB | Homo sapiens (human) | MRP-L11,Mitochondrial large ribosomal subunit protein uL11m |
| 19 | K | 39S ribosomal protein L13, mitochondrial | polymer | 178 | 20723.0 | 1 | UniProt (Q9BYD1) Pfam (PF00572) In PDB | Homo sapiens (human) | MRP-L13,Mitochondrial large ribosomal subunit protein uL13m |
| 20 | L | 39S ribosomal protein L14, mitochondrial | polymer | 145 | 15973.7 | 1 | UniProt (Q6P1L8) Pfam (PF00238) In PDB | Homo sapiens (human) | MRP-L14,39S ribosomal protein L32,mitochondrial,MRP-L32,Mitochondrial large ribosomal subunit protein uL14m |
| 21 | M | 39S ribosomal protein L15, mitochondrial | polymer | 296 | 33473.8 | 1 | UniProt (Q9P015) Pfam (PF00828) In PDB | Homo sapiens (human) | MRP-L15,Mitochondrial large ribosomal subunit protein uL15m |
| 22 | N | 39S ribosomal protein L16, mitochondrial | polymer | 251 | 28496.3 | 1 | UniProt (Q9NX20) Pfam (PF00252) In PDB | Homo sapiens (human) | MRP-L16,Mitochondrial large ribosomal subunit protein uL16m |
| 23 | O | 39S ribosomal protein L17, mitochondrial | polymer | 175 | 20083.3 | 1 | UniProt (Q9NRX2) Pfam (PF01196) In PDB | Homo sapiens (human) | MRP-L17,LYST-interacting protein 2,Mitochondrial large ribosomal subunit protein bL17m |
| 24 | P | Mitochondrial ribosomal protein L18, isoform CRA_b | polymer | 179 | 20465.3 | 1 | UniProt (A8K9D2) Pfam (PF00861) In PDB | Homo sapiens (human) | cDNA FLJ76688,highly similar to Homo sapiens HSPC071 mRNA |
| 25 | Q | 39S ribosomal protein L19, mitochondrial | polymer | 292 | 33585.0 | 1 | UniProt (P49406) Pfam (PF01245) In PDB | Homo sapiens (human) | MRP-L19,39S ribosomal protein L15,mitochondrial,MRP-L15,Mitochondrial large ribosomal subunit protein bL19m |
| 26 | R | 39S ribosomal protein L20, mitochondrial | polymer | 149 | 17479.7 | 1 | UniProt (Q9BYC9) Pfam (PF00453) In PDB | Homo sapiens (human) | MRP-L20,Mitochondrial large ribosomal subunit protein bL20m |
| 27 | S | 39S ribosomal protein L21, mitochondrial | polymer | 205 | 22847.7 | 1 | UniProt (Q7Z2W9) Pfam (PF00829) In PDB | Homo sapiens (human) | MRP-L21,Mitochondrial large ribosomal subunit protein bL21m |
| 28 | T | 39S ribosomal protein L22, mitochondrial | polymer | 212 | 24369.5 | 1 | UniProt (E7ESL0) Pfam (PF00237) In PDB | Homo sapiens (human) | |
| 29 | U | 39S ribosomal protein L23, mitochondrial | polymer | 153 | 17807.2 | 1 | UniProt (Q16540) Pfam (PF00276) In PDB | Homo sapiens (human) | MRP-L23,L23 mitochondrial-related protein,Mitochondrial large ribosomal subunit protein uL23m,Ribosomal protein L23-like |
| 30 | V | 39S ribosomal protein L24, mitochondrial | polymer | 216 | 24953.9 | 1 | UniProt (Q96A35) Pfam (PF00467) Pfam (PF17136) In PDB | Homo sapiens (human) | MRP-L24,Mitochondrial large ribosomal subunit protein uL24m |
| 31 | W | 39S ribosomal protein L27, mitochondrial | polymer | 148 | 16102.9 | 1 | UniProt (Q9P0M9) Pfam (PF01016) In PDB | Homo sapiens (human) | MRP-L27,Mitochondrial large ribosomal subunit protein bL27m |
| 32 | X | 39S ribosomal protein L28, mitochondrial | polymer | 256 | 30090.7 | 1 | UniProt (Q13084) Pfam (PF00830) In PDB | Homo sapiens (human) | MRP-L28,Melanoma antigen p15,Melanoma-associated antigen recognized by T-lymphocytes,Mitochondrial large ribosomal subunit protein bL28m |
| 33 | Y | 39S ribosomal protein L47, mitochondrial | polymer | 250 | 29508.5 | 1 | UniProt (Q9HD33) Pfam (PF06984) In PDB | Homo sapiens (human) | MRP-L47,Mitochondrial large ribosomal subunit protein uL29m,Nasopharyngeal carcinoma metastasis-related protein 1 |
| 34 | Z | 39S ribosomal protein L30, mitochondrial | polymer | 161 | 18582.8 | 1 | UniProt (Q8TCC3) Pfam (PF00327) In PDB | Homo sapiens (human) | MRP-L30,39S ribosomal protein L28,mitochondrial,MRP-L28,Mitochondrial large ribosomal subunit protein uL30m |
| 35 | a | 39S ribosomal protein L42, mitochondrial | polymer | 142 | 16691.2 | 1 | UniProt (Q9Y6G3) Pfam (PF10210) In PDB | Homo sapiens (human) | MRP-L42,39S ribosomal protein L31,mitochondrial,MRP-L31,Mitochondrial large ribosomal subunit protein mL42 |
| 36 | b | 39S ribosomal protein L43, mitochondrial | polymer | 215 | 23457.8 | 1 | UniProt (Q8N983) Pfam (PF05047) In PDB | Homo sapiens (human) | MRP-L43,Mitochondrial large ribosomal subunit protein mL43,Mitochondrial ribosomal protein bMRP36a |
| 37 | c | 39S ribosomal protein L44, mitochondrial | polymer | 332 | 37583.3 | 1 | UniProt (Q9H9J2) Pfam (PF22935) Pfam (PF22892) In PDB | Homo sapiens (human) | MRP-L44,Mitochondrial large ribosomal subunit protein mL44 |
| 38 | d | 39S ribosomal protein L45, mitochondrial | polymer | 306 | 35344.9 | 1 | UniProt (Q9BRJ2) Pfam (PF04280) In PDB | Homo sapiens (human) | MRP-L45,Mitochondrial large ribosomal subunit protein mL45 |
| 39 | e | 39S ribosomal protein L46, mitochondrial | polymer | 279 | 31748.1 | 1 | UniProt (Q9H2W6) Pfam (PF11788) In PDB | Homo sapiens (human) | MRP-L46,Mitochondrial large ribosomal subunit protein mL46,P2ECSL |
| 40 | f | 39S ribosomal protein L48, mitochondrial | polymer | 212 | 23970.8 | 1 | UniProt (Q96GC5) Pfam (PF00338) In PDB | Homo sapiens (human) | MRP-L48,Mitochondrial large ribosomal subunit protein mL48 |
| 41 | g | 39S ribosomal protein L49, mitochondrial | polymer | 166 | 19225.0 | 1 | UniProt (Q13405) Pfam (PF05046) In PDB | Homo sapiens (human) | MRP-L49,Mitochondrial large ribosomal subunit protein mL49,Neighbor of FAU,NOF,Protein NOF1 |
| 42 | h | 39S ribosomal protein L50, mitochondrial | polymer | 158 | 18349.9 | 1 | UniProt (Q8N5N7) Pfam (PF10501) In PDB | Homo sapiens (human) | MRP-L50,Mitochondrial large ribosomal subunit protein mL50 |
| 43 | i | 39S ribosomal protein L51, mitochondrial | polymer | 128 | 15125.9 | 1 | UniProt (Q4U2R6) Pfam (PF10244) In PDB | Homo sapiens (human) | MRP-L51,Mitochondrial large ribosomal subunit protein mL51,bMRP-64,bMRP64 |
| 44 | j | cDNA FLJ76418, highly similar to Homo sapiens mitochondrial ribosomal protein L52 (MRPL52), transcript variant 1, mRNA | polymer | 123 | 13696.7 | 1 | UniProt (A8K7J6) Pfam (PF18699) In PDB | Homo sapiens (human) | |
| 45 | k | 39S ribosomal protein L53, mitochondrial | polymer | 112 | 12125.9 | 1 | UniProt (Q96EL3) Pfam (PF10780) In PDB | Homo sapiens (human) | MRP-L53,Mitochondrial large ribosomal subunit protein mL53 |
| 46 | l | 39S ribosomal protein L54, mitochondrial | polymer | 138 | 15844.2 | 1 | UniProt (Q6P161) Pfam (PF08561) In PDB | Homo sapiens (human) | MRP-L54,Mitochondrial large ribosomal subunit protein mL54 |
| 47 | m | 39S ribosomal protein L55, mitochondrial | polymer | 128 | 15160.4 | 1 | UniProt (Q7Z7F7) Pfam (PF09776) In PDB | Homo sapiens (human) | MRP-L55,Mitochondrial large ribosomal subunit protein bL31m,Mitochondrial large ribosomal subunit protein mL55 |
| 48 | o | Ribosomal protein 63, mitochondrial | polymer | 102 | 12292.3 | 1 | UniProt (Q9BQC6) Pfam (PF14978) In PDB | Homo sapiens (human) | hMRP63,Mitochondrial large ribosomal subunit protein mL63,Mitochondrial ribosomal protein 63,Mitochondrial ribosomal protein L57 |
| 49 | p | Peptidyl-tRNA hydrolase ICT1, mitochondrial | polymer | 206 | 23674.2 | 1 | UniProt (Q14197) Pfam (PF00472) In PDB | Homo sapiens (human) | 39S ribosomal protein L58,mitochondrial,MRP-L58,Digestion substraction 1,DS-1,Immature colon carcinoma transcript 1 protein,Mitochondrial large ribosomal subunit protein mL62 |
| 50 | q | Growth arrest and DNA damage-inducible proteins-interacting protein 1 | polymer | 222 | 25426.9 | 1 | UniProt (Q8TAE8) Pfam (PF10147) In PDB | Homo sapiens (human) | 39S ribosomal protein L59,mitochondrial,MRP-L59,CKII beta-associating protein,CR6-interacting factor 1,CRIF1,Mitochondrial large ribosomal subunit protein mL64,Papillomavirus L2-interacting nuclear protein 1,PLINP-1,p53-responsive gene 6 protein |
| 51 | r | 39S ribosomal protein S18a, mitochondrial | polymer | 196 | 22224.1 | 1 | UniProt (Q9NVS2) Pfam (PF01084) In PDB | Homo sapiens (human) | S18mt-a,39S ribosomal protein S18-3,mitochondrial,MRP-S18-3,Mitochondrial large ribosomal subunit protein bS18a,Mitochondrial large ribosomal subunit protein mL66 |
| 52 | s | 39S ribosomal protein S30, mitochondrial | polymer | 439 | 50429.6 | 1 | UniProt (Q9NP92) Pfam (PF07147) In PDB | Homo sapiens (human) | S30mt,Mitochondrial large ribosomal subunit protein mL65,Mitochondrial large ribosomal subunit protein mS30,Programmed cell death protein 9 |
| 53 | C | Quinupristin | polymer | 8 | 1024.2 | 1 | BIRD (PRD_000505) | synthetic construct | |
| 54 | 0, 4, I | ZINC ION | non-polymer | 65.4 | 3 | Chemie (ZN) | |||
| 55 | A, 9, D, L, M... | MAGNESIUM ION | non-polymer | 24.3 | 134 | Chemie (MG) | |||
| 56 | A | GUANOSINE-5'-MONOPHOSPHATE | non-polymer | 363.2 | 1 | Chemie (G) | |||
| 57 | A | Virginiamycin M | non-polymer | 523.6 | 1 | Chemie (H8T) |
Sequence modifications
A: 1672 - 3229 (GenBank: 1391841121)
X: 1 - 256 (UniProt: Q13084)
d: 8 - 306 (UniProt: Q9BRJ2)
| PDB | External Database | Details |
|---|---|---|
| A 2360 | U 2347 | conflict |
| C 2361 | G 2348 | conflict |
| PDB | External Database | Details |
|---|---|---|
| Ala 148 | Thr 148 | conflict |
| Ser 149 | Pro 149 | conflict |
| Gly 150 | Lys 150 | conflict |
| PDB | External Database | Details |
|---|---|---|
| Phe 62 | Glu 55 | conflict |
| Ala 63 | Phe 56 | conflict |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 53 |
| Total formula weight | 1740904.3 | |
| Non-Polymers* | Number of molecules | 139 |
| Total formula weight | 4339.9 | |
| All* | Total formula weight | 1745244.2 |
