Research workbench
Staphylococcus aureus 50S after 30 minutes incubation a 37C
Analyse Staphylococcus aureus 50S after 30 minutes incubation a 37C in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ASN
- Type
- protein + RNA
- Length
- 5,393 residues
- Chains
- 25
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 23S; 5S; 50S ribosomal protein L33; 50S ribosomal protein L34; 50S ribosomal protein L35…
- UniProt
- A0A077V2P0, W8TQ59, A0A077UL47, B3VKN3, W8U3W0, W8TRC7, W8TUE6, A0A077UGA7, A0A077V4G0, A0A077UUA0, W8TRE0, A0A077UVB6, A0A077VMP6, D7URR3, A0A6I4H7Y4, W8TUB4, W8TRD5, A0A133Q8Z9, A0A077ULC5, A0A077URJ8, A0A077W1J5, W8UVN7, A0A1Q8DAT0
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 25 distinct chains · 20% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 23S | rna | 2742 | — | — |
| B | 5S | rna | 106 | — | — |
| 1 | 50S ribosomal protein L33 | protein | 47 | 0% helix, 43% strand | A0A077V2P0 |
| 2 | 50S ribosomal protein L34 | protein | 43 | 56% helix, 0% strand | W8TQ59 |
| 3 | 50S ribosomal protein L35 | protein | 64 | 27% helix, 13% strand | A0A077UL47 |
| F | 50S ribosomal protein L2 | protein | 274 | 4% helix, 27% strand | B3VKN3 |
| D | 50S ribosomal protein L3 | protein | 215 | 7% helix, 34% strand | W8U3W0 |
| E | 50S ribosomal protein L4 | protein | 206 | 29% helix, 15% strand | W8TRC7 |
| H | 50S ribosomal protein L13 | protein | 144 | 26% helix, 22% strand | W8TUE6 |
| L | 50S ribosomal protein L15 | protein | 146 | 16% helix, 8% strand | A0A077UGA7 |
| Y | 50S ribosomal protein L16 | protein | 137 | 20% helix, 23% strand | A0A077V4G0 |
| G | 50S ribosomal protein L14 | protein | 122 | 8% helix, 32% strand | A0A077UUA0 |
| M | 50S ribosomal protein L18 | protein | 117 | 30% helix, 16% strand | W8TRE0 |
| N | 50S ribosomal protein L19 | protein | 113 | 12% helix, 36% strand | A0A077UVB6 |
| O | 50S ribosomal protein L20 | protein | 116 | 78% helix, 0% strand | A0A077VMP6 |
| P | 50S ribosomal protein L21 | protein | 102 | 0% helix, 59% strand | D7URR3 |
| Q | 50S ribosomal protein L22 | protein | 112 | 31% helix, 34% strand | A0A6I4H7Y4 |
| R | 50S ribosomal protein L23 | protein | 89 | 21% helix, 38% strand | W8TUB4 |
| S | 50S ribosomal protein L24 | protein | 103 | 3% helix, 30% strand | W8TRD5 |
| T | 50S ribosomal protein L25 | protein | 94 | 17% helix, 32% strand | A0A133Q8Z9 |
| a | 50S ribosomal protein L27 | protein | 79 | 0% helix, 33% strand | A0A077ULC5 |
| V | 50S ribosomal protein L28 | protein | 49 | 10% helix, 45% strand | A0A077URJ8 |
| W | 50S ribosomal protein L29 | protein | 67 | 69% helix, 0% strand | A0A077W1J5 |
| X | 50S ribosomal protein L30 | protein | 58 | 31% helix, 22% strand | W8UVN7 |
| b | 50S ribosomal protein L32 | protein | 48 | 15% helix, 8% strand | A0A1Q8DAT0 |
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 | 892 | 0.88 | 0.92 | 96 | empty |
| 2 | 1045 | 0.87 | 0.89 | 90 | empty |
| 3 | 1012 | 0.87 | 0.89 | 77 | empty |
| 4 | 1131 | 0.87 | 0.88 | 99 | empty |
| 5 | 490 | 0.86 | 0.93 | 80 | empty |
Interfaces
45 interfaces between chains.
- A–F · 6368 Ų buried · 127 hydrogen bonds · protein-nucleic
- A–D · 5027 Ų buried · 85 hydrogen bonds · protein-nucleic
- A–L · 4411 Ų buried · 86 hydrogen bonds · protein-nucleic
- A–E · 4290 Ų buried · 63 hydrogen bonds · protein-nucleic
- A–O · 3960 Ų buried · 84 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 3 modified, 2 disulfide (nucleotide modification, disulfide).
Compared structures
- 7ASN · Staphylococcus aureus 50S after 30 minutes incubation a 37C · the same entry in another collection · chain R against R, 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 A0A077V2P0
- Every structure of UniProt W8TQ59
- Every structure of UniProt A0A077UL47
- Every structure of UniProt B3VKN3
- Every structure of UniProt W8U3W0
- Every structure of UniProt W8TRC7
- Every structure of UniProt W8TUE6
- Every structure of UniProt A0A077UGA7
- Every structure of UniProt A0A077V4G0
- Every structure of UniProt A0A077UUA0
- Every structure of UniProt W8TRE0
- Every structure of UniProt A0A077UVB6
- Every structure of UniProt A0A077VMP6
- Every structure of UniProt D7URR3
- Every structure of UniProt A0A6I4H7Y4
- Every structure of UniProt W8TUB4
- Every structure of UniProt W8TRD5
- Every structure of UniProt A0A133Q8Z9
- Every structure of UniProt A0A077ULC5
- Every structure of UniProt A0A077URJ8
- Every structure of UniProt A0A077W1J5
- Every structure of UniProt W8UVN7
- Every structure of UniProt A0A1Q8DAT0
- Elsewhere: RCSB PDB 7ASN · PDBe 7ASN · UniProt A0A077V2P0 · UniProt W8TQ59 · UniProt A0A077UL47 · UniProt B3VKN3 · UniProt W8U3W0 · UniProt W8TRC7 · UniProt W8TUE6 · UniProt A0A077UGA7 · UniProt A0A077V4G0 · UniProt A0A077UUA0 · UniProt W8TRE0 · UniProt A0A077UVB6 · UniProt A0A077VMP6 · UniProt D7URR3 · UniProt A0A6I4H7Y4 · UniProt W8TUB4 · UniProt W8TRD5 · UniProt A0A133Q8Z9 · UniProt A0A077ULC5 · UniProt A0A077URJ8 · UniProt A0A077W1J5 · UniProt W8UVN7 · UniProt A0A1Q8DAT0
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