MolNFT v1 · #169691 · protein
Crystal structure of sr-related and ctd-associated factor 4(SCAF4- CID)WITH peptide S2,S5P-ctd
6XKB: “Crystal structure of sr-related and ctd-associated factor 4(SCAF4- CID)WITH peptide S2,S5P-ctd”. X-ray diffraction, 2 ligands (BTN, UNX), 7 pockets (best druggability 0.75). MolNFT v1 #169691 on GenesisL1: 3D structure, binding…
- PDB
- 6XKB
- Type
- protein
- Length
- 755 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sr-related and ctd-associated factor 4; S2,S5P-ctd peptide
- UniProt
- O95104
- Ligands
- BTN, UNX
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · 6 distinct chains · 77% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sr-related and ctd-associated factor 4 | protein | 136 | 80% helix, 1% strand | O95104 |
| B | Sr-related and ctd-associated factor 4 | protein | 138 | 78% helix, 1% strand | O95104 |
| C | Sr-related and ctd-associated factor 4 | protein | 139 | 77% helix, 1% strand | O95104 |
| D | Sr-related and ctd-associated factor 4 | protein | 135 | 79% helix, 1% strand | O95104 |
| E | Sr-related and ctd-associated factor 4 | protein | 137 | 80% helix, 1% strand | O95104 |
| F, G, I, J, K | S2,S5P-ctd peptide | protein | 14 | 0% helix, 7% strand | — |
Ligands and binding sites
- BTN · Biotin · ligand · 2 copies · chains E, I, C, K
- UNX · Unknown atom or ion · ion · 12 copies · chains A, B, C, D, J, I, E, F, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 830 | 0.75 | 0.79 | 81 | UNX |
| 2 | 714 | 0.69 | 0.76 | 54 | empty |
| 3 | 170 | 0.55 | 0.80 | 24 | UNX |
| 4 | 190 | 0.52 | 0.78 | 27 | empty |
| 5 | 160 | 0.49 | 0.78 | 22 | empty |
Interfaces
16 interfaces between chains.
- A–G · 829 Ų buried · 18 hydrogen bonds · protein-protein
- E–K · 814 Ų buried · 17 hydrogen bonds · protein-protein
- D–J · 813 Ų buried · 14 hydrogen bonds · protein-protein
- C–I · 806 Ų buried · 18 hydrogen bonds · protein-protein
- B–F · 783 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 modified, 2 cofactor (phosphorylation, biotinylation).
Compared structures
- 6XKB · Crystal structure of SR-related and CTD-associated factor 4(SCAF4-CID)with peptide… · the same entry in another collection · chain K against K, TM-score 1.00
- O95104 · AlphaFold monomer V2.0 prediction for sr-related and ctd-associated factor 4 (O95104) · a predicted model of the same protein · chain D against A, TM-score 0.99
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 O95104
- Elsewhere: RCSB PDB 6XKB · PDBe 6XKB · UniProt O95104
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