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Co-crystal structure of cca-phe-caproic acid-biotin and sparsomycin bound to the 50S ribosomal subunit
Analyse Co-crystal structure of cca-phe-caproic acid-biotin and sparsomycin bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1M90
- Type
- protein + RNA
- Length
- 6,580 residues
- Chains
- 31
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 23S rRNA; 5S rRNA; Cca; Ribosomal protein L2; Ribosomal protein L3; Ribosomal protein L4…
- UniProt
- P20276, P20279, P12735, P14124, P14135, P12743, P15825, P29198, P22450, P12737, P14123, P12733, P14119, P12734, P10970, P12732, P10972, P14116, P10971, P14121, P18138, P12736, P32410, P22452, P32411
- Ligands
- SPS, PHA, ACA, MG, NA, CD, K, CL
- Pockets
- 20 · best druggability 0.90
Structure
x-ray diffraction · 31 distinct chains · 29% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 23S rRNA | rna | 2754 | — | — |
| B | 5S rRNA | rna | 122 | — | — |
| 5 | Cca | rna | 3 | — | — |
| C | Ribosomal protein L2 | protein | 237 | 12% helix, 24% strand | P20276 |
| D | Ribosomal protein L3 | protein | 337 | 14% helix, 32% strand | P20279 |
| E | Ribosomal protein L4 | protein | 246 | 33% helix, 14% strand | P12735 |
| F | Ribosomal protein L5 | protein | 140 | 24% helix, 20% strand | P14124 |
| G | Ribosomal protein L6 | protein | 172 | 22% helix, 42% strand | P14135 |
| H | Ribosomal protein L7AE | protein | 119 | 48% helix, 13% strand | P12743 |
| I | Ribosomal protein L10 | protein | 29 | 79% helix, 0% strand | P15825 |
| J | Ribosomal protein L10E | protein | 156 | 15% helix, 28% strand | — |
| K | Ribosomal protein L13 | protein | 142 | 40% helix, 15% strand | P29198 |
| L | Ribosomal protein L14 | protein | 132 | 5% helix, 38% strand | P22450 |
| M | Ribosomal protein L15 | protein | 145 | 19% helix, 16% strand | P12737 |
| N | Ribosomal protein L15E | protein | 194 | 34% helix, 16% strand | — |
| O | Ribosomal protein L18 | protein | 186 | 39% helix, 13% strand | P14123 |
| P | Ribosomal protein L18E | protein | 115 | 46% helix, 23% strand | P12733 |
| Q | Ribosomal protein L19E | protein | 143 | 62% helix, 4% strand | P14119 |
| R | Ribosomal protein L21E | protein | 95 | 14% helix, 32% strand | P12734 |
| S | Ribosomal protein L22 | protein | 150 | 35% helix, 31% strand | P10970 |
| T | Ribosomal protein L23 | protein | 81 | 35% helix, 31% strand | P12732 |
| U | Ribosomal protein L24 | protein | 119 | 29% helix, 29% strand | P10972 |
| V | Ribosomal protein L24E | protein | 53 | 21% helix, 19% strand | P14116 |
| W | Ribosomal protein L29 | protein | 65 | 74% helix, 0% strand | P10971 |
| X | Ribosomal protein L30 | protein | 154 | 38% helix, 14% strand | P14121 |
| Y | Ribosomal protein L31E | protein | 82 | 43% helix, 28% strand | P18138 |
| Z | Ribosomal protein L32E | protein | 142 | 23% helix, 12% strand | P12736 |
| 1 | Ribosomal protein L37AE | protein | 73 | 37% helix, 18% strand | — |
| 2 | Ribosomal protein L37E | protein | 56 | 13% helix, 16% strand | P32410 |
| 3 | Ribosomal protein L39E | protein | 46 | 41% helix, 0% strand | P22452 |
| 4 | Ribosomal protein L44E | protein | 92 | 14% helix, 33% strand | P32411 |
Ligands and binding sites
- SPS · Sparsomycin · ligand · chains A, 5
- PHA · Phenylalaninal · ligand · chains A, 5
- ACA · 6-aminohexanoic acid · ligand · chains A
- MG · Magnesium ion · metal · 119 copies · chains A, C, E, D, 2, N, T, S, X, B, V, 3, Z, 4, Q, 5, L, U, 1
- NA · Sodium ion · metal · 86 copies · chains A, M, J, D, 3, Z, S, B, K, E, N, 4, F, C, R, T, U
- CD · Cadmium ion · metal · 5 copies · chains P, V, 1, 2, 4
- K · Potassium ion · metal · 2 copies · chains A, N
- CL · Chloride ion · ion · 22 copies · chains A, 3, R, L, M, K, Z, C, D, G, N, F, O, P, S, 4
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 | 1073 | 0.90 | 0.92 | 99 | MG, NA |
| 2 | 953 | 0.88 | 0.91 | 118 | MG, CL |
| 3 | 752 | 0.86 | 0.91 | 73 | empty |
| 4 | 1132 | 0.86 | 0.88 | 101 | MG, NA |
| 5 | 816 | 0.86 | 0.89 | 75 | CL |
Interfaces
54 interfaces between chains.
- A–D · 7363 Ų buried · 226 hydrogen bonds · protein-nucleic
- A–N · 6900 Ų buried · 179 hydrogen bonds · protein-nucleic
- A–C · 6278 Ų buried · 171 hydrogen bonds · protein-nucleic
- A–E · 5577 Ų buried · 137 hydrogen bonds · protein-nucleic
- A–Q · 4360 Ų buried · 125 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 1M90 · Co-crystal structure of CCA-Phe-caproic acid-biotin and sparsomycin bound to the 50S… · the same entry in another collection · chain 5 against 5, 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 P20276
- Every structure of UniProt P20279
- 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
- Every structure of UniProt P32410
- Every structure of UniProt P22452
- Every structure of UniProt P32411
- Elsewhere: RCSB PDB 1M90 · PDBe 1M90 · UniProt P20276 · UniProt P20279 · 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 · UniProt P32410 · UniProt P22452 · UniProt P32411
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