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Structure of the SH2 domain of the candida glabrata transcription elongation factor SPT6, crystal form a

Analyse Structure of the SH2 domain of the candida glabrata transcription elongation… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3GXW
Type: protein
Length: 386 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transcription elongation factor SPT6
UniProt: Q6FLB1
Ligands: NA
Pockets: 9 · best druggability 0.57

Structure

x-ray diffraction · 4 distinct chains · 28% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Transcription elongation factor SPT6	protein	93	27% helix, 32% strand	Q6FLB1
B	Transcription elongation factor SPT6	protein	94	28% helix, 34% strand	Q6FLB1
C	Transcription elongation factor SPT6	protein	100	27% helix, 34% strand	Q6FLB1
D	Transcription elongation factor SPT6	protein	99	29% helix, 34% strand	Q6FLB1

Ligands and binding sites

NA · Sodium ion · metal · 4 copies · chains A, B, C, D
SIN · Succinic acid · additive · 2 copies · chains A, C

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

Pockets

9 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	85	0.57	0.87	19	empty
2	351	0.56	0.75	26	empty
3	165	0.54	0.80	23	empty
4	176	0.53	0.79	21	empty
5	90	0.45	0.80	25	empty

Interfaces

5 interfaces between chains.

B–C · 706 Å² buried · 2 hydrogen bonds · protein-protein
A–D · 694 Å² buried · 2 hydrogen bonds · protein-protein
A–B · 642 Å² buried · 3 hydrogen bonds · protein-protein
B–D · 190 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 119 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 modified (engineered).

Compared structures

3GXW · Structure of the SH2 domain of the Candida glabrata transcription elongation factor Spt6… · the same entry in another collection · chain D against D, TM-score 1.00
Q6FLB1 · AlphaFold monomer V2.0 prediction for transcription elongation factor SPT6 (Q6FLB1) · a predicted model of the same protein · chain D against A, TM-score 0.83

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 Q6FLB1
Elsewhere: RCSB PDB 3GXW · PDBe 3GXW · UniProt Q6FLB1

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