MolNFT v1 · #152409 · protein
Cryo-EM structure of human srcap complex
6IGM · Ruvb-like 1: “Cryo-EM structure of human srcap complex”. Electron microscopy, 20 pockets (best druggability 0.89). MolNFT v1 #152409 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6IGM
- Type
- protein
- Length
- 3,116 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ruvb-like 1; Ruvb-like 2; Actin-related protein 6; Helicase srcap; Unknown subunit
- EC
- 3.6.4.12, 3.6.4.-
- UniProt
- Q9Y265, Q9Y230, Q9GZN1, Q6ZRS2
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 9 distinct chains · 35% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ruvb-like 1 (EC 3.6.4.12) | protein | 405 | 38% helix, 16% strand | Q9Y265 |
| B | Ruvb-like 2 (EC 3.6.4.12) | protein | 398 | 34% helix, 17% strand | Q9Y230 |
| C | Ruvb-like 1 (EC 3.6.4.12) | protein | 370 | 37% helix, 17% strand | Q9Y265 |
| D | Ruvb-like 2 (EC 3.6.4.12) | protein | 396 | 35% helix, 17% strand | Q9Y230 |
| E | Ruvb-like 1 (EC 3.6.4.12) | protein | 380 | 39% helix, 19% strand | Q9Y265 |
| F | Ruvb-like 2 (EC 3.6.4.12) | protein | 366 | 34% helix, 17% strand | Q9Y230 |
| G | Actin-related protein 6 | protein | 366 | 30% helix, 12% strand | Q9GZN1 |
| H | Helicase srcap (EC 3.6.4.-) | protein | 373 | 36% helix, 7% strand | Q6ZRS2 |
| X | Unknown subunit | protein | 62 | 13% helix, 0% strand | — |
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 | 1005 | 0.89 | 0.90 | 126 | empty |
| 2 | 827 | 0.88 | 0.91 | 109 | empty |
| 3 | 1018 | 0.85 | 0.85 | 107 | empty |
| 4 | 829 | 0.84 | 0.86 | 78 | empty |
| 5 | 801 | 0.84 | 0.87 | 99 | empty |
Interfaces
20 interfaces between chains.
- A–F · 3201 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 3189 Ų buried · 21 hydrogen bonds · protein-protein
- D–E · 3172 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 2808 Ų buried · 32 hydrogen bonds · protein-protein
- E–F · 2503 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 6IGM · Cryo-EM Structure of Human SRCAP Complex · the same entry in another collection · chain X against X, TM-score 1.00
- Q9GZN1 · AlphaFold monomer V2.0 prediction for actin-related protein 6 (Q9GZN1) · a predicted model of the same protein · chain G against A, TM-score 0.91
- Q9Y265 · AlphaFold monomer V2.0 prediction for ruvb-like 1 (Q9Y265) · a predicted model of the same protein · chain C against A, TM-score 0.81
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 Q9Y265
- Every structure of UniProt Q9Y230
- Every structure of UniProt Q9GZN1
- Every structure of UniProt Q6ZRS2
- Elsewhere: RCSB PDB 6IGM · PDBe 6IGM · UniProt Q9Y265 · UniProt Q9Y230 · UniProt Q9GZN1 · UniProt Q6ZRS2
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