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Crystal structure of human RTF1 PLUS3 domain in complex with SPT5 ctr phosphopeptide

Analyse Crystal structure of human RTF1 PLUS3 domain in complex with SPT5 ctr… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4L1U
Type: protein
Length: 827 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA polymerase-associated protein RTF1 homolog; Transcription elongation factor SPT5
UniProt: Q92541, O00267
Ligands: SO4
Pockets: 11 · best druggability 0.74

Structure

x-ray diffraction · 9 distinct chains · 36% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RNA polymerase-associated protein RTF1 homolog	protein	130	38% helix, 34% strand	Q92541
B	RNA polymerase-associated protein RTF1 homolog	protein	134	36% helix, 38% strand	Q92541
C	RNA polymerase-associated protein RTF1 homolog	protein	130	37% helix, 34% strand	Q92541
D	RNA polymerase-associated protein RTF1 homolog	protein	136	37% helix, 38% strand	Q92541
E, F	RNA polymerase-associated protein RTF1 homolog	protein	134	36% helix, 38% strand	Q92541
G	Transcription elongation factor SPT5	protein	8	0% helix, 0% strand	O00267
H	Transcription elongation factor SPT5	protein	11	27% helix, 0% strand	O00267
I	Transcription elongation factor SPT5	protein	5	0% helix, 0% strand	O00267
J	Transcription elongation factor SPT5	protein	5	0% helix, 0% strand	O00267

Ligands and binding sites

SO4 · Sulfate ion · ion · 29 copies · chains A, H, B, D, G, C, E, I, F, J
GOL · Glycerol · additive · 4 copies · chains A, C, B, D, F

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	782	0.74	0.79	61	empty
2	227	0.56	0.79	38	SO4
3	107	0.55	0.84	22	empty
4	200	0.53	0.78	39	SO4
5	120	0.42	0.76	18	empty

Interfaces

15 interfaces between chains.

C–F · 600 Å² buried · 8 hydrogen bonds · protein-protein
B–E · 575 Å² buried · 10 hydrogen bonds · protein-protein
C–H · 567 Å² buried · 12 hydrogen bonds · protein-protein
B–D · 475 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 469 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (phosphorylation).

Compared structures

4L1U · Crystal Structure of Human Rtf1 Plus3 Domain in Complex with Spt5 CTR Phosphopeptide · the same entry in another collection · chain J against J, TM-score 1.00
Q92541 · AlphaFold monomer V2.0 prediction for RNA polymerase-associated protein RTF1 homolog… · a predicted model of the same protein · chain E against A, TM-score 0.98

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 Q92541
Every structure of UniProt O00267
Elsewhere: RCSB PDB 4L1U · PDBe 4L1U · UniProt Q92541 · UniProt O00267

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