MolNFT v2 · #151351 · protein + RNA
Structure of a partial yeast 48S preinitiation complex in open conformation.
6GSM: “Structure of a partial yeast 48S preinitiation complex in open conformation.”. Electron microscopy at 5.15, 4 ligands (7NO, GCP, MG). MolNFT v2 #151351 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6GSM
- Type
- protein + RNA
- Length
- 9,927 residues
- Chains
- 47
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 5.15
- Source
- Kluyveromyces lactis NRRL Y-1140; Saccharomyces cerevisiae S288C; SYNTHETIC…
- UniProt
- Q6CN12, Q6CWD0, Q6CKL3, Q6CRK7, Q6CWJ2, Q6CRA3, Q6CM04, Q6CTD6, Q6CMG3, Q6CM18, Q6CVZ5, Q6CX80, Q6CLU4, Q6CJK0, P27069, Q6CKV4, Q875N2, Q6CWU3, Q6CWT9, Q6CXM0, Q6CIM1, Q6CXT6, Q6CW21, F2Z602, Q6CU44, Q6CW78, Q6CS01, Q6CNL2, P33285, Q6CPG3, Q6CUH5, P69061, Q6CNI7, P0CX86, P38912, P20459, P32481, P09064, P32911, P38249, P06103, P32497, P40217, Q04067
- Ligands
- 7NO, GCP, MG, ZN
Structure
electron microscopy · resolution 5.15 · 47 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1 | — | rna | 74 | — | — |
| 2 | — | rna | 1798 | — | — |
| A | — | protein | 208 | — | Q6CN12 |
| 3 | — | rna | 3 | — | — |
| B | — | protein | 222 | — | Q6CWD0 |
| C | — | protein | 217 | — | Q6CKL3 |
| D | — | protein | 223 | — | Q6CRK7 |
| E | — | protein | 260 | — | Q6CWJ2 |
| F | — | protein | 206 | — | Q6CRA3 |
| G | — | protein | 226 | — | Q6CM04 |
| H | — | protein | 184 | — | Q6CTD6 |
| I | — | protein | 188 | — | Q6CMG3 |
| J | — | protein | 182 | — | Q6CM18 |
| K | — | protein | 96 | — | Q6CVZ5 |
| L | — | protein | 155 | — | Q6CX80 |
| M | — | protein | 117 | — | Q6CLU4 |
| N | — | protein | 150 | — | Q6CJK0 |
| O | — | protein | 127 | — | P27069 |
| P | — | protein | 119 | — | Q6CKV4 |
| Q | — | protein | 141 | — | Q875N2 |
| R | — | protein | 111 | — | Q6CWU3 |
| S | — | protein | 145 | — | Q6CWT9 |
| T | — | protein | 143 | — | Q6CXM0 |
| U | — | protein | 106 | — | Q6CIM1 |
| V | — | protein | 87 | — | Q6CXT6 |
| W | — | protein | 129 | — | Q6CW21 |
| X | — | protein | 144 | — | F2Z602 |
| Y | — | protein | 134 | — | Q6CU44 |
| Z | — | protein | 70 | — | Q6CW78 |
| a | — | protein | 98 | — | Q6CS01 |
| b | — | protein | 81 | — | Q6CNL2 |
| c | — | protein | 62 | — | P33285 |
| d | — | protein | 53 | — | Q6CPG3 |
| e | — | protein | 58 | — | Q6CUH5 |
| f | — | protein | 69 | — | P69061 |
| g | — | protein | 309 | — | Q6CNI7 |
| h | — | protein | 25 | — | P0CX86 |
| i | — | protein | 95 | — | P38912 |
| j | — | protein | 249 | — | P20459 |
| k | — | protein | 414 | — | P32481 |
| l | — | protein | 130 | — | P09064 |
| m | — | protein | 96 | — | P32911 |
| o | — | protein | 528 | — | P38249 |
| p | — | protein | 651 | — | P06103 |
| q | — | protein | 665 | — | P32497 |
| s | — | protein | 330 | — | P40217 |
| r | — | protein | 49 | — | Q04067 |
Ligands and binding sites
- 7NO · [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-2-(phosphonooxymethyl)oxolan-3-yl] (2~{S})-2-azanyl-4-methylsulfanyl-butanoate · ligand · chains 1, k
- GCP · Phosphomethylphosphonic acid guanylate ester · ligand · chains k, l
- MG · Magnesium ion · metal · 82 copies · chains 2, O, G, p, D, T, U, C, Q, k
- ZN · Zinc ion · metal · 4 copies · chains O, a, b, q, f, l
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Compared structures
- P40217 · AlphaFold monomer V2.0 prediction for eukaryotic translation initiation factor 3 subunit… · a predicted model of the same protein · chain s against A, TM-score 0.99
- Q04067 · AlphaFold monomer V2.0 prediction for eukaryotic translation initiation factor 3 subunit… · a predicted model of the same protein · chain r against A, TM-score 0.97
- P32481 · AlphaFold monomer V2.0 prediction for eukaryotic translation initiation factor 2 subunit… · a predicted model of the same protein · chain k against A, TM-score 0.92
- Q6CWD0 · AlphaFold monomer V2.0 prediction for 40S ribosomal protein S1 (Q6CWD0) · a predicted model of the same protein · chain B against A, TM-score 0.92
- P20459 · AlphaFold monomer V2.0 prediction for eukaryotic translation initiation factor 2 subunit… · a predicted model of the same protein · chain j against A, TM-score 0.89
- P38912 · AlphaFold monomer V2.0 prediction for eukaryotic translation initiation factor 1A (P38912) · a predicted model of the same protein · chain i against A, TM-score 0.88
- P09064 · AlphaFold monomer V2.0 prediction for eukaryotic translation initiation factor 2 subunit… · a predicted model of the same protein · chain l against A, TM-score 0.86
- P38249 · AlphaFold monomer V2.0 prediction for eukaryotic translation initiation factor 3 subunit… · a predicted model of the same protein · chain o against A, TM-score 0.79
- P06103 · AlphaFold monomer V2.0 prediction for eukaryotic translation initiation factor 3 subunit… · a predicted model of the same protein · chain p against A, TM-score 0.77
- P32497 · AlphaFold monomer V2.0 prediction for eukaryotic translation initiation factor 3 subunit… · a predicted model of the same protein · chain q against A, TM-score 0.75
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 Q6CN12
- Every structure of UniProt Q6CWD0
- Every structure of UniProt Q6CKL3
- Every structure of UniProt Q6CRK7
- Every structure of UniProt Q6CWJ2
- Every structure of UniProt Q6CRA3
- Every structure of UniProt Q6CM04
- Every structure of UniProt Q6CTD6
- Every structure of UniProt Q6CMG3
- Every structure of UniProt Q6CM18
- Every structure of UniProt Q6CVZ5
- Every structure of UniProt Q6CX80
- Every structure of UniProt Q6CLU4
- Every structure of UniProt Q6CJK0
- Every structure of UniProt P27069
- Every structure of UniProt Q6CKV4
- Every structure of UniProt Q875N2
- Every structure of UniProt Q6CWU3
- Every structure of UniProt Q6CWT9
- Every structure of UniProt Q6CXM0
- Every structure of UniProt Q6CIM1
- Every structure of UniProt Q6CXT6
- Every structure of UniProt Q6CW21
- Every structure of UniProt F2Z602
- Every structure of UniProt Q6CU44
- Every structure of UniProt Q6CW78
- Every structure of UniProt Q6CS01
- Every structure of UniProt Q6CNL2
- Every structure of UniProt P33285
- Every structure of UniProt Q6CPG3
- Every structure of UniProt Q6CUH5
- Every structure of UniProt P69061
- Every structure of UniProt Q6CNI7
- Every structure of UniProt P0CX86
- Every structure of UniProt P38912
- Every structure of UniProt P20459
- Every structure of UniProt P32481
- Every structure of UniProt P09064
- Every structure of UniProt P32911
- Every structure of UniProt P38249
- Every structure of UniProt P06103
- Every structure of UniProt P32497
- Every structure of UniProt P40217
- Every structure of UniProt Q04067
- Elsewhere: RCSB PDB 6GSM · PDBe 6GSM · UniProt Q6CN12 · UniProt Q6CWD0 · UniProt Q6CKL3 · UniProt Q6CRK7 · UniProt Q6CWJ2 · UniProt Q6CRA3 · UniProt Q6CM04 · UniProt Q6CTD6 · UniProt Q6CMG3 · UniProt Q6CM18 · UniProt Q6CVZ5 · UniProt Q6CX80 · UniProt Q6CLU4 · UniProt Q6CJK0 · UniProt P27069 · UniProt Q6CKV4 · UniProt Q875N2 · UniProt Q6CWU3 · UniProt Q6CWT9 · UniProt Q6CXM0 · UniProt Q6CIM1 · UniProt Q6CXT6 · UniProt Q6CW21 · UniProt F2Z602 · UniProt Q6CU44 · UniProt Q6CW78 · UniProt Q6CS01 · UniProt Q6CNL2 · UniProt P33285 · UniProt Q6CPG3 · UniProt Q6CUH5 · UniProt P69061 · UniProt Q6CNI7 · UniProt P0CX86 · UniProt P38912 · UniProt P20459 · UniProt P32481 · UniProt P09064 · UniProt P32911 · UniProt P38249 · UniProt P06103 · UniProt P32497 · UniProt P40217 · UniProt Q04067
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