Research workbench
Mammalian 48S late-stage initiation complex with beta-globin mRNA
Analyse Mammalian 48S late-stage initiation complex with beta-globin mRNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YAL
- Type
- protein + RNA
- Length
- 8,183 residues
- Chains
- 41
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Initiator methionylated tRNA; 60S ribosomal protein UL41; 40S ribosomal protein US2; 40S…
- UniProt
- A0A087WNH4, G1TLT8, G1TN72, G1TNM3, G1TK17, U3KMN4, G1TM55, G1SVB0, G1TJW1, B7NZS8, G1TPV3, G1TRM4, G1SFR8, G1SP51, G1T1F0, G1SGX4, G1TU13, G1TN62, G1SIZ2, G1TM82, G1TG89, G1SZ47, G1TS40, G1TFE8, G1TZ76, G1TIB4, G1U7M4, G1SK22, G1SJB4, G1TDB3, G1T8A2, G1T2G4, G1TPG3, G1U0Q2
- Ligands
- SF4, GNP, MG
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 41 distinct chains · 26% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1 | Initiator methionylated tRNA | rna | 75 | — | — |
| l | 60S ribosomal protein UL41 | protein | 25 | 92% helix, 0% strand | A0A087WNH4 |
| C | 40S ribosomal protein US2 | protein | 208 | 30% helix, 13% strand | G1TLT8 |
| D | 40S ribosomal protein ES1 | protein | 215 | 26% helix, 26% strand | G1TN72 |
| E | 40S ribosomal protein US5 | protein | 226 | 31% helix, 25% strand | — |
| F | 40S ribosomal protein US3 | protein | 227 | 32% helix, 27% strand | G1TNM3 |
| G | 40S ribosomal protein ES4 | protein | 263 | 11% helix, 29% strand | G1TK17 |
| H | 40S ribosomal protein US7 | protein | 191 | 45% helix, 8% strand | U3KMN4 |
| I | 40S ribosomal protein ES6 | protein | 237 | 30% helix, 22% strand | G1TM55 |
| J | 40S ribosomal protein ES7 | protein | 190 | 28% helix, 15% strand | G1SVB0 |
| K | 40S ribosomal protein ES8 | protein | 206 | 21% helix, 21% strand | G1TJW1 |
| L | 40S ribosomal protein US4 | protein | 182 | 48% helix, 4% strand | B7NZS8 |
| M | 40S ribosomal protein ES10 | protein | 98 | 34% helix, 16% strand | G1TPV3 |
| N | 40S ribosomal protein US17 | protein | 158 | 3% helix, 28% strand | G1TRM4 |
| O | 40S ribosomal protein ES12 | protein | 124 | 41% helix, 7% strand | G1SFR8 |
| P | 40S ribosomal protein US15 | protein | 150 | 52% helix, 0% strand | G1SP51 |
| Q | 40S ribosomal protein US11 | protein | 136 | 24% helix, 14% strand | G1T1F0 |
| S | 40S ribosomal protein US9 | protein | 141 | 35% helix, 20% strand | G1SGX4 |
| T | 40S ribosomal protein ES17 | protein | 126 | 44% helix, 1% strand | G1TU13 |
| V | 40S ribosomal protein ES19 | protein | 141 | 45% helix, 10% strand | G1TN62 |
| W | 40S ribosomal protein US10 | protein | 104 | 23% helix, 40% strand | G1SIZ2 |
| X | 40S ribosomal protein ES21 | protein | 82 | 20% helix, 12% strand | G1TM82 |
| Y | 40S ribosomal protein US8 | protein | 129 | 30% helix, 29% strand | G1TG89 |
| Z | 40S ribosomal protein US12 | protein | 142 | 21% helix, 20% strand | G1SZ47 |
| a | 40S ribosomal protein ES24 | protein | 126 | 28% helix, 25% strand | G1TS40 |
| b | 40S ribosomal protein ES26 | protein | 99 | 11% helix, 23% strand | G1TFE8 |
| c | 40S ribosomal protein ES27 | protein | 84 | 0% helix, 14% strand | G1TZ76 |
| d | 40S ribosomal protein ES28 | protein | 64 | 0% helix, 45% strand | G1TIB4 |
| e | 40S ribosomal protein US14 | protein | 53 | 8% helix, 4% strand | G1U7M4 |
| f | 40S ribosomal protein ES31 | protein | 71 | 0% helix, 14% strand | G1SK22 |
| g | Ribosomal protein RACK1 | protein | 313 | 0% helix, 51% strand | G1SJB4 |
| n | 40S ribosomal protein ES25 | protein | 75 | 40% helix, 12% strand | G1TDB3 |
| i | 40S ribosomal protein ES30 | protein | 59 | 17% helix, 0% strand | G1T8A2 |
| 2 | 18S ribosomal RNA | rna | 1744 | — | — |
| A | Eukaryotic translation initiation factor 2 subunit alpha | protein | 266 | 35% helix, 15% strand | G1T2G4 |
| B | Eukaryotic translation initiation factor 2 subunit gamma | protein | 422 | 14% helix, 36% strand | — |
| j | Eukaryotic translation initiation factor 1A | protein | 109 | 13% helix, 20% strand | — |
| k | ATP-binding cassette sub-family E member 1 (ABCE1) | protein | 595 | 26% helix, 14% strand | — |
| U | 40S ribosomal protein US13 | protein | 145 | 43% helix, 7% strand | G1TPG3 |
| R | 40S ribosomal protein US19 | protein | 140 | 23% helix, 12% strand | G1U0Q2 |
| 3 | Beta-globin mRNA | rna | 42 | — | — |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains k
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 2 copies · chains k
- MG · Magnesium ion · metal · chains k
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1072 | 0.89 | 0.92 | 125 | empty |
| 2 | 1111 | 0.89 | 0.91 | 112 | empty |
| 3 | 923 | 0.86 | 0.88 | 101 | empty |
| 4 | 1141 | 0.86 | 0.88 | 89 | empty |
| 5 | 454 | 0.86 | 0.94 | 67 | empty |
Interfaces
126 interfaces between chains.
- I–2 · 5552 Ų buried · 118 hydrogen bonds · protein-nucleic
- K–2 · 4274 Ų buried · 93 hydrogen bonds · protein-nucleic
- G–2 · 4160 Ų buried · 63 hydrogen bonds · protein-nucleic
- Z–2 · 3546 Ų buried · 66 hydrogen bonds · protein-nucleic
- L–2 · 3278 Ų buried · 51 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified, 1 covalent, 1 disulfide (nucleotide modification, covalent ligand, disulfide).
Compared structures
- 6YAL · Mammalian 48S late-stage initiation complex with beta-globin mRNA · the same entry in another collection · chain S against S, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt A0A087WNH4
- Every structure of UniProt G1TLT8
- Every structure of UniProt G1TN72
- Every structure of UniProt G1TNM3
- Every structure of UniProt G1TK17
- Every structure of UniProt U3KMN4
- Every structure of UniProt G1TM55
- Every structure of UniProt G1SVB0
- Every structure of UniProt G1TJW1
- Every structure of UniProt B7NZS8
- Every structure of UniProt G1TPV3
- Every structure of UniProt G1TRM4
- Every structure of UniProt G1SFR8
- Every structure of UniProt G1SP51
- Every structure of UniProt G1T1F0
- Every structure of UniProt G1SGX4
- Every structure of UniProt G1TU13
- Every structure of UniProt G1TN62
- Every structure of UniProt G1SIZ2
- Every structure of UniProt G1TM82
- Every structure of UniProt G1TG89
- Every structure of UniProt G1SZ47
- Every structure of UniProt G1TS40
- Every structure of UniProt G1TFE8
- Every structure of UniProt G1TZ76
- Every structure of UniProt G1TIB4
- Every structure of UniProt G1U7M4
- Every structure of UniProt G1SK22
- Every structure of UniProt G1SJB4
- Every structure of UniProt G1TDB3
- Every structure of UniProt G1T8A2
- Every structure of UniProt G1T2G4
- Every structure of UniProt G1TPG3
- Every structure of UniProt G1U0Q2
- Elsewhere: RCSB PDB 6YAL · PDBe 6YAL · UniProt A0A087WNH4 · UniProt G1TLT8 · UniProt G1TN72 · UniProt G1TNM3 · UniProt G1TK17 · UniProt U3KMN4 · UniProt G1TM55 · UniProt G1SVB0 · UniProt G1TJW1 · UniProt B7NZS8 · UniProt G1TPV3 · UniProt G1TRM4 · UniProt G1SFR8 · UniProt G1SP51 · UniProt G1T1F0 · UniProt G1SGX4 · UniProt G1TU13 · UniProt G1TN62 · UniProt G1SIZ2 · UniProt G1TM82 · UniProt G1TG89 · UniProt G1SZ47 · UniProt G1TS40 · UniProt G1TFE8 · UniProt G1TZ76 · UniProt G1TIB4 · UniProt G1U7M4 · UniProt G1SK22 · UniProt G1SJB4 · UniProt G1TDB3 · UniProt G1T8A2 · UniProt G1T2G4 · UniProt G1TPG3 · UniProt G1U0Q2
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