6VZ5
Escherichia coli transcription-translation complex D3 (TTC-D3) containing mRNA with a 21 nt long spacer, NusG, and fMet-tRNAs at E-site and P-site
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 | 50S ribosomal protein L21 | polymer | 103 | 11586.4 | 1 | UniProt (D7ZEN7) Pfam (PF00829) UniProt (by SIFTS) (P0AG48) In PDB | Escherichia coli | |
2 | 1 | 50S ribosomal protein L22 | polymer | 110 | 12253.4 | 1 | UniProt (D7Z9G0) Pfam (PF00237) UniProt (by SIFTS) (P61175) In PDB | Escherichia coli | |
3 | 2 | 50S ribosomal protein L23 | polymer | 100 | 11222.2 | 1 | UniProt (D7X2Z9) Pfam (PF00276) UniProt (by SIFTS) (P0ADZ0) In PDB | Escherichia coli | |
4 | 3 | 50S ribosomal protein L24 | polymer | 104 | 11339.3 | 1 | UniProt (D7Z9G6) Pfam (PF00467) Pfam (PF17136) UniProt (by SIFTS) (P60624) In PDB | Escherichia coli | |
5 | 4 | 50S ribosomal protein L25 | polymer | 94 | 10713.5 | 1 | UniProt (D7XH79) Pfam (PF01386) UniProt (by SIFTS) (P68919) In PDB | Escherichia coli | |
6 | 5 | NT DNA | polymer | 36 | 11042.1 | 1 | Escherichia coli | ||
7 | 6 | T DNA | polymer | 36 | 10956.0 | 1 | Escherichia coli | ||
8 | 7 | mRNA with 21 nt long spacer | polymer | 38 | 11993.8 | 1 | Escherichia coli | ||
9 | A, B | E-site and P-site tRNA (fMet) | polymer | 76 | 24496.6 | 2 | Escherichia coli | ||
10 | AA | DNA-directed RNA polymerase subunit beta | polymer | 1342 | 150820.9 | 1 | UniProt (P0A8V4) Pfam (PF04565) Pfam (PF10385) Pfam (PF00562) Pfam (PF04560) Pfam (PF04563) Pfam (PF04561) UniProt (by SIFTS) (P0A8V2) In PDB | Escherichia coli | RNAP subunit beta,RNA polymerase subunit beta,Transcriptase subunit beta |
11 | AB | Transcription termination/antitermination protein NusG | polymer | 181 | 20560.5 | 1 | UniProt (V8K3D7) Pfam (PF02357) Pfam (PF00467) UniProt (by SIFTS) (P0AFG0) In PDB | Escherichia coli | |
12 | AC, AD | DNA-directed RNA polymerase subunit alpha | polymer | 329 | 36558.7 | 2 | UniProt (A0A073G207) Pfam (PF01193) Pfam (PF01000) Pfam (PF03118) UniProt (by SIFTS) (P0A7Z4) In PDB | Escherichia coli | RNAP subunit alpha,RNA polymerase subunit alpha,Transcriptase subunit alpha |
13 | AE | DNA-directed RNA polymerase subunit beta' | polymer | 1407 | 155366.8 | 1 | UniProt (A0A4S1NBU2) Pfam (PF04997) Pfam (PF00623) Pfam (PF04983) Pfam (PF05000) Pfam (PF04998) UniProt (by SIFTS) (P0A8T7) In PDB | Escherichia coli | RNAP subunit beta',RNA polymerase subunit beta',Transcriptase subunit beta' |
14 | AF | DNA-directed RNA polymerase subunit omega | polymer | 91 | 10249.5 | 1 | UniProt (P0A802) Pfam (PF01192) UniProt (by SIFTS) (P0A800) In PDB | Escherichia coli | RNAP omega subunit,RNA polymerase omega subunit,Transcriptase subunit omega |
15 | C | 30S ribosomal protein S18 | polymer | 75 | 9005.5 | 1 | UniProt (A0A0E2KXL3) Pfam (PF01084) UniProt (by SIFTS) (P0A7T7) In PDB | Escherichia coli | |
16 | D | 16S rRNA | polymer | 1542 | 499690.0 | 1 | GenBank (1732209707) | Escherichia coli | |
17 | E | 30S ribosomal protein S20 | polymer | 87 | 9708.5 | 1 | UniProt (D7ZAS2) Pfam (PF01649) UniProt (by SIFTS) (P0A7U7) In PDB | Escherichia coli | |
18 | F | 30S ribosomal protein S21 | polymer | 71 | 8524.0 | 1 | UniProt (A0A0E2L2J1) Pfam (PF01165) UniProt (by SIFTS) (P68679) In PDB | Escherichia coli | |
19 | G | 30S ribosomal protein S2 | polymer | 241 | 26781.7 | 1 | UniProt (D7ZK99) Pfam (PF00318) UniProt (by SIFTS) (P0A7V0) In PDB | Escherichia coli | |
20 | H | 30S ribosomal protein S1 | polymer | 557 | 61238.9 | 1 | UniProt (A0A1X3LHG1) Pfam (PF00575) UniProt (by SIFTS) (P0AG67) In PDB | Escherichia coli | |
21 | I | 30S ribosomal protein S3 | polymer | 233 | 26031.3 | 1 | UniProt (B7MCS9) Pfam (PF07650) Pfam (PF00189) UniProt (by SIFTS) (P0A7V3) In PDB | Escherichia coli | |
22 | J | 30S ribosomal protein S4 | polymer | 206 | 23514.2 | 1 | UniProt (D7Z9H7) Pfam (PF00163) Pfam (PF01479) UniProt (by SIFTS) (P0A7V8) In PDB | Escherichia coli | |
23 | K | 30S ribosomal protein S5 | polymer | 167 | 17629.4 | 1 | UniProt (D7Z9H2) Pfam (PF00333) Pfam (PF03719) UniProt (by SIFTS) (P0A7W1) In PDB | Escherichia coli | |
24 | L | 30S ribosomal protein S6 | polymer | 135 | 15727.5 | 1 | UniProt (P02358) Pfam (PF01250) In PDB | Escherichia coli | Small ribosomal subunit protein bS6 |
25 | M | 30S ribosomal protein S7 | polymer | 179 | 20055.2 | 1 | UniProt (A0A5Q2GFB5) Pfam (PF00177) UniProt (by SIFTS) (P02359) In PDB | Escherichia coli | |
26 | N | 30S ribosomal protein S8 | polymer | 130 | 14146.6 | 1 | UniProt (D7Z9G9) Pfam (PF00410) UniProt (by SIFTS) (P0A7W7) In PDB | Escherichia coli | |
27 | O | 30S ribosomal protein S9 | polymer | 130 | 14886.3 | 1 | UniProt (D7ZES9) Pfam (PF00380) UniProt (by SIFTS) (P0A7X3) In PDB | Escherichia coli | |
28 | P | 30S ribosomal protein S10 | polymer | 103 | 11755.6 | 1 | UniProt (D7Z9F4) Pfam (PF00338) UniProt (by SIFTS) (P0A7R5) In PDB | Escherichia coli | |
29 | Q | 30S ribosomal protein S11 | polymer | 117 | 12487.2 | 1 | UniProt (P0A7R9) Pfam (PF00411) In PDB | Escherichia coli | Small ribosomal subunit protein uS11 |
30 | R | 30S ribosomal protein S12 | polymer | 124 | 13768.2 | 1 | UniProt (D7ZAN0) Pfam (PF00164) UniProt (by SIFTS) (P0A7S3) In PDB | Escherichia coli | |
31 | S | 30S ribosomal protein S14 | polymer | 101 | 11606.6 | 1 | UniProt (D7Z9G8) Pfam (PF00253) UniProt (by SIFTS) (P0AG59) In PDB | Escherichia coli | |
32 | T | 30S ribosomal protein S15 | polymer | 89 | 10290.8 | 1 | UniProt (D7ZEL4) Pfam (PF00312) UniProt (by SIFTS) (P0ADZ4) In PDB | Escherichia coli | |
33 | U | 30S ribosomal protein S16 | polymer | 82 | 9207.6 | 1 | UniProt (B7MIU7) Pfam (PF00886) UniProt (by SIFTS) (P0A7T3) In PDB | Escherichia coli | |
34 | V | 30S ribosomal protein S17 | polymer | 84 | 9724.5 | 1 | UniProt (D7Z9G4) Pfam (PF00366) UniProt (by SIFTS) (P0AG63) In PDB | Escherichia coli | |
35 | W | 30S ribosomal protein S19 | polymer | 92 | 10455.4 | 1 | UniProt (D7Z9F9) Pfam (PF00203) UniProt (by SIFTS) (P0A7U3) In PDB | Escherichia coli | |
36 | X | 30S ribosomal protein S13 | polymer | 118 | 13128.5 | 1 | UniProt (H4UQ02) Pfam (PF00416) UniProt (by SIFTS) (P0A7S9) In PDB | Escherichia coli | |
37 | Y | mRNA in the ribosomal RNA entrance pore | polymer | 3 | 873.5 | 1 | Escherichia coli | ||
38 | a | 23S rRNA | polymer | 2904 | 941635.4 | 1 | GenBank (937521852) | Escherichia coli | |
39 | b | 50S ribosomal protein L27 | polymer | 85 | 9146.5 | 1 | UniProt (P0A7L8) Pfam (PF01016) In PDB | Escherichia coli | Large ribosomal subunit protein bL27 |
40 | c | 50S ribosomal protein L28 | polymer | 78 | 9027.6 | 1 | UniProt (S0YB49) Pfam (PF00830) UniProt (by SIFTS) (P0A7M2) In PDB | Escherichia coli | |
41 | d | 5S rRNA | polymer | 120 | 38790.1 | 1 | GenBank (1273279017) | Escherichia coli | |
42 | e | 50S ribosomal protein L29 | polymer | 63 | 7286.5 | 1 | UniProt (D7Z9G3) Pfam (PF00831) UniProt (by SIFTS) (P0A7M6) In PDB | Escherichia coli | |
43 | f | 50S ribosomal protein L30 | polymer | 59 | 6554.8 | 1 | UniProt (D7Z9H3) Pfam (PF00327) UniProt (by SIFTS) (P0AG51) In PDB | Escherichia coli | |
44 | g | 50S ribosomal protein L31 | polymer | 70 | 7887.1 | 1 | UniProt (D7ZFP6) Pfam (PF01197) UniProt (by SIFTS) (P0A7M9) In PDB | Escherichia coli | |
45 | h | 50S ribosomal protein L2 | polymer | 273 | 29923.6 | 1 | UniProt (P60422) Pfam (PF00181) Pfam (PF03947) In PDB | Escherichia coli | Large ribosomal subunit protein uL2 |
46 | i | 50S ribosomal protein L32 | polymer | 57 | 6463.4 | 1 | UniProt (D7ZGG2) Pfam (PF01783) UniProt (by SIFTS) (P0A7N4) In PDB | Escherichia coli | |
47 | j | 50S ribosomal protein L3 | polymer | 209 | 22277.5 | 1 | UniProt (P60438) Pfam (PF00297) In PDB | Escherichia coli | Large ribosomal subunit protein uL3 |
48 | k | 50S ribosomal protein L33 | polymer | 55 | 6388.6 | 1 | UniProt (D7Z9P0) Pfam (PF00471) UniProt (by SIFTS) (P0A7N9) In PDB | Escherichia coli | |
49 | l | 50S ribosomal protein L4 | polymer | 201 | 22121.6 | 1 | UniProt (D7Z9F6) Pfam (PF00573) UniProt (by SIFTS) (P60723) In PDB | Escherichia coli | |
50 | m | 50S ribosomal protein L34 | polymer | 46 | 5397.5 | 1 | UniProt (B7MGC4) Pfam (PF00468) UniProt (by SIFTS) (P0A7P5) In PDB | Escherichia coli | |
51 | n | 50S ribosomal protein L5 | polymer | 179 | 20333.6 | 1 | UniProt (D7Z9G7) Pfam (PF00281) Pfam (PF00673) UniProt (by SIFTS) (P62399) In PDB | Escherichia coli | |
52 | o | 50S ribosomal protein L35 | polymer | 65 | 7313.0 | 1 | UniProt (D7Z814) Pfam (PF01632) UniProt (by SIFTS) (P0A7Q1) In PDB | Escherichia coli | |
53 | p | 50S ribosomal protein L6 | polymer | 177 | 18932.8 | 1 | UniProt (D7Z9H0) Pfam (PF00347) UniProt (by SIFTS) (P0AG55) In PDB | Escherichia coli | |
54 | q | 50S ribosomal protein L36 | polymer | 38 | 4377.4 | 1 | UniProt (A0A0E2L017) Pfam (PF00444) UniProt (by SIFTS) (P0A7Q6) In PDB | Escherichia coli | |
55 | r | 50S ribosomal protein L9 | polymer | 149 | 15789.0 | 1 | UniProt (D7ZI15) Pfam (PF01281) Pfam (PF03948) UniProt (by SIFTS) (P0A7R1) In PDB | Escherichia coli | |
56 | s | 50S ribosomal protein L13 | polymer | 142 | 16050.6 | 1 | UniProt (D7ZET0) Pfam (PF00572) UniProt (by SIFTS) (P0AA10) In PDB | Escherichia coli | |
57 | t | 50S ribosomal protein L14 | polymer | 123 | 13565.1 | 1 | UniProt (D7Z9G5) Pfam (PF00238) UniProt (by SIFTS) (P0ADY3) In PDB | Escherichia coli | |
58 | u | 50S ribosomal protein L15 | polymer | 144 | 15008.5 | 1 | UniProt (A0A037Y8L6) Pfam (PF00828) UniProt (by SIFTS) (P02413) In PDB | Escherichia coli | |
59 | v | 50S ribosomal protein L16 | polymer | 136 | 15312.3 | 1 | UniProt (P0ADY7) Pfam (PF00252) In PDB | Escherichia coli | Large ribosomal subunit protein uL16 |
60 | w | 50S ribosomal protein L17 | polymer | 127 | 14393.7 | 1 | UniProt (A0A1X3LC97) Pfam (PF01196) UniProt (by SIFTS) (P0AG44) In PDB | Escherichia coli | |
61 | x | 50S ribosomal protein L18 | polymer | 117 | 12794.7 | 1 | UniProt (D7Z9H1) Pfam (PF00861) UniProt (by SIFTS) (P0C018) In PDB | Escherichia coli | |
62 | y | 50S ribosomal protein L19 | polymer | 115 | 13159.3 | 1 | UniProt (D7ZKU3) Pfam (PF01245) UniProt (by SIFTS) (P0A7K6) In PDB | Escherichia coli | |
63 | z | 50S ribosomal protein L20 | polymer | 118 | 13528.0 | 1 | UniProt (B7MAS6) Pfam (PF00453) UniProt (by SIFTS) (P0A7L3) In PDB | Escherichia coli | |
64 | AE | MAGNESIUM ION | non-polymer | 24.3 | 1 | Chemie (MG) | |||
65 | AE | ZINC ION | non-polymer | 65.4 | 2 | Chemie (ZN) |
Sequence modifications
AE: 1 - 1407 (UniProt: A0A4S1NBU2)
a: 1 - 2904 (GenBank: 937521852)
PDB | External Database | Details |
---|---|---|
Val 1384 | Met 1384 | conflict |
PDB | External Database | Details |
---|---|---|
A 887 | U 472128 | conflict |
Sequence viewer
Contents of the asymmetric unit
Polymers | Number of chains | 65 |
Total formula weight | 2693909.8 | |
Non-Polymers* | Number of molecules | 3 |
Total formula weight | 155.1 | |
All* | Total formula weight | 2694064.9 |