UniProt P62987
Ubiquitin-60S ribosomal protein L40 (P62987)
Ubiquitin-60S ribosomal protein L40 (UniProt P62987), EC 2.3.2.24: 87 experimental structures and 1 predicted model on GenesisL1, 5 ligands bound, 56 pockets. Binding sites, druggability and experiment against prediction…
- UniProt
- P62987
- Protein
- Ubiquitin-60S ribosomal protein L40
- EC
- 2.3.2.24
- Experimental structures
- 87
- Predicted models
- 1
- Ligands
- 5
- Pockets
- 56 · 21 records with a druggable one
Structures
88 records of P62987 in the MolNFT archive: 87 experimental, 1 predicted.
| Entry | Title | Method | Chains | Ligands | Pockets |
|---|---|---|---|---|---|
| 2LJ5 | Description of the Structural fluctuations of proteins from structure-based calculations of… | solution nmr | A | — | — |
| 2LJ5 | Description of the structural fluctuations of proteins from structure- based calculations of… | solution nmr | A | — | — |
| 2MJB | Solution nmr structure of ubiquitin refined against dipolar couplings in 4 media | solution nmr | A | — | — |
| 2MJB | Solution NMR structure of ubiquitin refined against dipolar couplings in 4 media | solution nmr | A | — | — |
| 2MUR | Solution Structure of the Human FAAP20 UBZ-Ubiquitin Complex | solution nmr | B | — | — |
| 2MUR | Solution structure of the human FAAP20 ubz-ubiquitin complex | solution nmr | B | — | — |
| 2N3U | Solution structure of the Rpn1 T1 site engaging two monoubiquitin molecules | solution nmr | B, C | — | — |
| 2N3U | Solution structure of the RPN1 T1 site engaging two monoubiquitin molecules | solution nmr | B, C | — | — |
| 2N3V | Solution structure of the Rpn1 T1 site with K48-linked diubiquitin in the extended binding mode | solution nmr | B, C | — | — |
| 2N3V | Solution structure of the RPN1 T1 site with K48-linked diubiquitin in the extended binding mode | solution nmr | B, C | — | — |
| 2N3W | Solution structure of the Rpn1 T1 site with K48-linked diubiquitin in the contracted binding mode | solution nmr | B, C | — | — |
| 2N3W | Solution structure of the RPN1 T1 site with K48-linked diubiquitin in the contracted binding mode | solution nmr | B, C | — | — |
| 4JIO | Bro1 V domain and ubiquitin | x-ray diffraction | U | — | — |
| 4JIO | BRO1 V domain and ubiquitin | x-ray diffraction | U | — | — |
| 4P4H | Caught-in-action signaling complex of RIG-I 2CARD domain and MAVS CARD domain | x-ray diffraction | S, T, U, W, X | — | — |
| 4P4H | Caught-in-action signaling complex of rig-I 2CARD domain and mavs card domain | x-ray diffraction | S, T, U, W, X | — | — |
| 4PIG | Crystal structure of the ubiquitin K11S mutant | x-ray diffraction | A, B, C, D | — | — |
| 4PIG | Crystal structure of the ubiquitin K11S mutant | x-ray diffraction | A, B, C, D | — | — |
| 4PIH | X-ray crystal structure of the K33S mutant of ubiquitin | x-ray diffraction | A, B | — | — |
| 4PIH | X-ray crystal structure of the K33S mutant of ubiquitin | x-ray diffraction | A, B | — | — |
| 4PIJ | X-ray crystal structure of the K11S/K63S double mutant of ubiquitin | x-ray diffraction | A, B | — | — |
| 4PIJ | X-ray crystal structure of the K11S/K63S double mutant of ubiquitin | x-ray diffraction | A, B | — | — |
| 4RF0 | Crystal structure of the Middle-East respiratory syndrome coronavirus papain-like protease in… | x-ray diffraction | B | — | — |
| 4RF0 | Crystal structure of the middle-east respiratory syndrome coronavirus papain-like protease in… | x-ray diffraction | B | — | — |
| 4RF1 | Crystal structure of the Middle-East respiratory syndrome coronavirus papain-like protease in… | x-ray diffraction | B | — | — |
| 4RF1 | Crystal structure of the middle-east respiratory syndrome coronavirus papain-like protease in… | x-ray diffraction | B | — | — |
| 4S1Z | Crystal structure of TRABID NZF1 in complex with K29 linked di-Ubiquitin | x-ray diffraction | A, B, C, D, E | — | — |
| 4S1Z | Crystal structure of trabid NZF1 in complex with K29 linked di- ubiquitin | x-ray diffraction | A, B, C, D, E | — | — |
| 4UG0 | Structure of the human 80S ribosome | electron microscopy | Lm | — | — |
| 4V6X | Structure of the human 80S ribosome | electron microscopy | Cm | — | — |
| 4XKL | Crystal structure of NDP52 ZF2 in complex with mono-ubiquitin | x-ray diffraction | A, C | — | — |
| 4XKL | Crystal structure of NDP52 ZF2 in complex with mono-ubiquitin | x-ray diffraction | A, C | — | — |
| 5LKS | Structure-function insights reveal the human ribosome as a cancer target for antibiotics | electron microscopy | Lm | ZN | — |
| 6IP8 | Cryo-EM structure of the HCV IRES dependently initiated CMV-stalled 80S ribosome (Structure iv) | electron microscopy | 2g | — | — |
| 6LQM | Cryo-EM structure of a pre-60S ribosomal subunit - state C | electron microscopy | R | — | — |
| 6OLE | Human ribosome nascent chain complex (CDH1-RNC) stalled by a drug-like molecule with AP and PE tRNAs | electron microscopy | n | — | — |
| 6OLF | Human ribosome nascent chain complex (CDH1-RNC) stalled by a drug-like molecule with AA and PE tRNAs | electron microscopy | n | — | 1 (best 0.88) |
| 6OLG | Human ribosome nascent chain complex stalled by a drug-like small molecule (CDH1_RNC with PP tRNA) | electron microscopy | Am | — | — |
| 6OLI | Structure of human ribosome nascent chain complex selectively stalled by a drug-like small molecule… | electron microscopy | n | — | — |
| 6OM0 | Human ribosome nascent chain complex (PCSK9-RNC) stalled by a drug-like molecule with AP and PE… | electron microscopy | n | — | 1 (best 0.88) |
| 6OM7 | Human ribosome nascent chain complex (PCSK9-RNC) stalled by a drug-like small molecule with AA and… | electron microscopy | n | — | — |
| 6QZP | High-resolution cryo-EM structure of the human 80S ribosome | electron microscopy | Lm | ZN | — |
| 6XA1 | Structure of a drug-like compound stalled human translation termination complex | electron microscopy | Lm | ZN | — |
| 6Y2L | Structure of human ribosome in POST state | electron microscopy | Lm | ZN | 1 (best 0.86) |
| 6Y6X | Tetracenomycin X bound to the human ribosome | electron microscopy | Lm | ZN | — |
| 6Z6L | Cryo-EM structure of human CCDC124 bound to 80S ribosomes | electron microscopy | Lm | ZN | — |
| 6Z6M | Cryo-EM structure of human 80S ribosomes bound to EBP1, eEF2 and SERBP1 | electron microscopy | Lm | ZN | — |
| 6ZMO | SARS-CoV-2 Nsp1 bound to the human LYAR-80S-eEF1a ribosome complex | electron microscopy | Lm | ZN | 1 (best 0.88) |
| 7AY1 | Cryo-EM structure of USP1-UAF1 bound to mono-ubiquitinated FANCD2, and FANCI | electron microscopy | C | — | 2 (best 0.73) |
| 7AY1 | Cryo-EM structure of USP1-UAF1 bound to mono-ubiquitinated FANCD2, and fanci | electron microscopy | C | — | — |
| 7F5S | human delta-METTL18 60S ribosome | electron microscopy | Lm | ZN | — |
| 7M3Q | Structure of the Smurf2 HECT Domain with a High Affinity Ubiquitin Variant (UbV) | x-ray diffraction | B | — | 1 (best 0.56) |
| 7M3Q | Structure of the SMURF2 hect domain with a high affinity ubiquitin variant (ubv) | x-ray diffraction | B | — | — |
| 7OWC | Structure of CYLD CAP-Gly3 (467-565) bound to Ub; orthorhobic space group | x-ray diffraction | A, C | — | 1 (best 0.71) |
| 7OWC | Structure of cyld cap-GLY3 (467-565) bound to ub; orthorhobic space group | x-ray diffraction | A, C | — | — |
| 7UN3 | Complex of UBE2O with NAP1L1 and ubiquitylated uL2 | electron microscopy | D, A | — | 14 (best 0.79) |
| 7UN3 | Complex of UBE2O with NAP1L1 and ubiquitylated UL2 | electron microscopy | D, A | — | — |
| 7XNX | High resolution cry-EM structure of the human 80S ribosome from SNORD127+/+ Kasumi-1 cells | electron microscopy | Lm | ZN | — |
| 7XNY | High resolution cry-EM structure of the human 80S ribosome from SNORD127+/- Kasumi-1 cells | electron microscopy | Lm | ZN | 1 (best 0.88) |
| 7ZF1 | Structure of ubiquitinated FANCI in complex with FANCD2 and double-stranded DNA | electron microscopy | C | — | 1 (best 0.86) |
28 records more on the page itself.
Ligands
- ZN · Zinc ion · in 32 records
- 3CN · 3-aminopropane · in 1 record
- AR6 · [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl [hydroxy-[[(2R,3S,4R,5S)-3,4,5-trihydroxyoxolan-2-yl]methoxy]phosphoryl] hydrogen phosphate · in 1 record
- BR · Bromide ion · in 1 record
- SO4 · Sulfate ion · in 1 record
Experiment against prediction
- 4S1Z chain E against the predicted model P62987: TM-score 0.98, RMSD 0.42 Å
- 4S1Z chain E against the predicted model P62987: TM-score 0.98, RMSD 0.42 Å
- 4P4H chain S against the predicted model P62987: TM-score 0.98, RMSD 0.45 Å
- 4P4H chain S against the predicted model P62987: TM-score 0.98, RMSD 0.45 Å
- 4S1Z chain A against the predicted model P62987: TM-score 0.98, RMSD 0.69 Å
- 4S1Z chain A against the predicted model P62987: TM-score 0.98, RMSD 0.69 Å
- 7OWC chain A against the predicted model P62987: TM-score 0.97, RMSD 0.53 Å
- 7OWC chain A against the predicted model P62987: TM-score 0.97, RMSD 0.53 Å
- 7OWC chain C against the predicted model P62987: TM-score 0.97, RMSD 0.52 Å
- 7OWC chain C against the predicted model P62987: TM-score 0.97, RMSD 0.52 Å
Elsewhere
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