Research workbench
Crystal structure of virginiamycin M and S bound to the 50S ribosomal subunit of haloarcula marismortui
Analyse Crystal structure of virginiamycin M and S bound to the 50S ribosomal subunit… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YIT
- Type
- protein + RNA
- Length
- 6,658 residues
- Chains
- 32
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 23S ribosomal RNA; 50S ribosomal protein L37E; 50S ribosomal protein L39E; 50S ribosomal…
- UniProt
- P32410, P22452, P32411, P20276, P12735, P14124, P14135, P12743, P15825, P29198, P22450, P12737, P14123, P12733, P14119, P12734, P10970, P12732, P10972, P14116, P10971, P14121, P18138, P12736
- Ligands
- VIR, MG, NA, CD, K, CL
- Pockets
- 20 · best druggability 0.90
Structure
x-ray diffraction · 32 distinct chains · 30% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 0 | 23S ribosomal RNA | rna | 2754 | — | — |
| 1 | 50S ribosomal protein L37E | protein | 56 | 13% helix, 11% strand | P32410 |
| 2 | 50S ribosomal protein L39E | protein | 46 | 41% helix, 0% strand | P22452 |
| 3 | 50S ribosomal protein L44E | protein | 92 | 14% helix, 32% strand | P32411 |
| 8 | Virginiamycin S1 | protein | 7 | 0% helix, 0% strand | — |
| 9 | 5S ribosomal RNA | rna | 122 | — | — |
| A | 50S ribosomal protein L2P | protein | 237 | 14% helix, 22% strand | P20276 |
| B | 50S ribosomal protein L3P | protein | 337 | 14% helix, 33% strand | — |
| C | 50S ribosomal protein L4E | protein | 246 | 33% helix, 14% strand | P12735 |
| D | 50S ribosomal protein L5P | protein | 140 | 24% helix, 21% strand | P14124 |
| E | 50S ribosomal protein L6P | protein | 172 | 23% helix, 41% strand | P14135 |
| F | 50S ribosomal protein L7AE | protein | 119 | 49% helix, 15% strand | P12743 |
| G | Acidic ribosomal protein P0 homolog | protein | 29 | 79% helix, 0% strand | P15825 |
| H | 50S ribosomal protein L10E | protein | 160 | 23% helix, 27% strand | — |
| I | 50S ribosomal protein L11P | protein | 70 | 41% helix, 3% strand | — |
| J | 50S ribosomal protein L13P | protein | 142 | 40% helix, 15% strand | P29198 |
| K | 50S ribosomal protein L14P | protein | 132 | 8% helix, 38% strand | P22450 |
| L | 50S ribosomal protein L15P | protein | 145 | 19% helix, 16% strand | P12737 |
| M | 50S ribosomal protein L15E | protein | 194 | 35% helix, 16% strand | — |
| N | 50S ribosomal protein L18P | protein | 186 | 40% helix, 12% strand | P14123 |
| O | 50S ribosomal protein L18E | protein | 115 | 46% helix, 23% strand | P12733 |
| P | 50S ribosomal protein L19E | protein | 143 | 61% helix, 4% strand | P14119 |
| Q | 50S ribosomal protein L21E | protein | 95 | 13% helix, 32% strand | P12734 |
| R | 50S ribosomal protein L22P | protein | 150 | 35% helix, 31% strand | P10970 |
| S | 50S ribosomal protein L23P | protein | 81 | 35% helix, 31% strand | P12732 |
| T | 50S ribosomal protein L24P | protein | 119 | 29% helix, 29% strand | P10972 |
| U | 50S ribosomal protein L24E | protein | 53 | 21% helix, 19% strand | P14116 |
| V | 50S ribosomal protein L29P | protein | 65 | 72% helix, 0% strand | P10971 |
| W | 50S ribosomal protein L30P | protein | 154 | 38% helix, 15% strand | P14121 |
| X | 50S ribosomal protein L31E | protein | 82 | 43% helix, 28% strand | P18138 |
| Y | 50S ribosomal protein L32E | protein | 142 | 23% helix, 12% strand | P12736 |
| Z | 50S ribosomal protein L37AE | protein | 73 | 33% helix, 19% strand | — |
Ligands and binding sites
- VIR · Virginiamycin M1 · ligand · chains 0, 8
- MG · Magnesium ion · metal · 118 copies · chains 0, A, C, B, S, R, W, 9, E, Y, 3, P, M, 8, 2, K, T
- NA · Sodium ion · metal · 85 copies · chains 0, L, H, B, 2, Y, R, T, 9, J, C, M, 3, D, A, Q, S
- CD · Cadmium ion · metal · 5 copies · chains 1, 3, O, U, Z
- K · Potassium ion · metal · chains 0, M
- CL · Chloride ion · ion · 22 copies · chains 0, 2, Q, K, L, J, Y, W, 3, A, B, E, M, D, N, O, R
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 | 1058 | 0.90 | 0.92 | 95 | MG, NA |
| 2 | 949 | 0.88 | 0.91 | 119 | MG, CL |
| 3 | 1176 | 0.87 | 0.88 | 117 | empty |
| 4 | 821 | 0.86 | 0.89 | 80 | CL |
| 5 | 1199 | 0.85 | 0.87 | 97 | MG |
Interfaces
55 interfaces between chains.
- 0–B · 7422 Ų buried · 230 hydrogen bonds · protein-nucleic
- 0–M · 6516 Ų buried · 182 hydrogen bonds · protein-nucleic
- 0–A · 6282 Ų buried · 189 hydrogen bonds · protein-nucleic
- 0–C · 5575 Ų buried · 139 hydrogen bonds · protein-nucleic
- 0–P · 4376 Ų buried · 128 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 10 modified (nonstandard, nucleotide modification).
Compared structures
- 1YIT · Crystal Structure Of Virginiamycin M and S Bound To The 50S Ribosomal Subunit Of… · the same entry in another collection · chain 1 against 1, 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 P32410
- Every structure of UniProt P22452
- Every structure of UniProt P32411
- Every structure of UniProt P20276
- Every structure of UniProt P12735
- Every structure of UniProt P14124
- Every structure of UniProt P14135
- Every structure of UniProt P12743
- Every structure of UniProt P15825
- Every structure of UniProt P29198
- Every structure of UniProt P22450
- Every structure of UniProt P12737
- Every structure of UniProt P14123
- Every structure of UniProt P12733
- Every structure of UniProt P14119
- Every structure of UniProt P12734
- Every structure of UniProt P10970
- Every structure of UniProt P12732
- Every structure of UniProt P10972
- Every structure of UniProt P14116
- Every structure of UniProt P10971
- Every structure of UniProt P14121
- Every structure of UniProt P18138
- Every structure of UniProt P12736
- Elsewhere: RCSB PDB 1YIT · PDBe 1YIT · UniProt P32410 · UniProt P22452 · UniProt P32411 · UniProt P20276 · UniProt P12735 · UniProt P14124 · UniProt P14135 · UniProt P12743 · UniProt P15825 · UniProt P29198 · UniProt P22450 · UniProt P12737 · UniProt P14123 · UniProt P12733 · UniProt P14119 · UniProt P12734 · UniProt P10970 · UniProt P12732 · UniProt P10972 · UniProt P14116 · UniProt P10971 · UniProt P14121 · UniProt P18138 · UniProt P12736
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