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Crystal structure of the yeast SEC2P gef domain

Analyse Crystal structure of the yeast SEC2P gef domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2E7S
Type: protein
Length: 2,313 residues
Chains: 20
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Rab guanine nucleotide exchange factor SEC2
UniProt: P17065
Pockets: 12 · best druggability 0.57

Structure

x-ray diffraction · 8 distinct chains · 82% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, I, L, P, T	Rab guanine nucleotide exchange factor SEC2	protein	114	81% helix, 0% strand	P17065
B	Rab guanine nucleotide exchange factor SEC2	protein	121	77% helix, 0% strand	P17065
C	Rab guanine nucleotide exchange factor SEC2	protein	118	73% helix, 0% strand	P17065
D, E, F, O	Rab guanine nucleotide exchange factor SEC2	protein	124	76% helix, 0% strand	P17065
G	Rab guanine nucleotide exchange factor SEC2	protein	110	89% helix, 0% strand	P17065
H, J	Rab guanine nucleotide exchange factor SEC2	protein	107	83% helix, 0% strand	P17065
K, M, S	Rab guanine nucleotide exchange factor SEC2	protein	117	82% helix, 0% strand	P17065
N, Q, R	Rab guanine nucleotide exchange factor SEC2	protein	111	96% helix, 0% strand	P17065

Pockets

12 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	306	0.57	0.76	32	empty
2	243	0.56	0.78	24	empty
3	89	0.55	0.86	22	empty
4	116	0.54	0.82	18	empty
5	133	0.50	0.79	25	empty

Interfaces

22 interfaces between chains.

E–F · 2334 Å² buried · 10 hydrogen bonds · protein-protein
K–L · 2117 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 2094 Å² buried · 14 hydrogen bonds · protein-protein
C–D · 2085 Å² buried · 16 hydrogen bonds · protein-protein
O–P · 2064 Å² buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 34 modified (engineered).

Compared structures

2E7S · Crystal structure of the yeast Sec2p GEF domain · the same entry in another collection · chain J against J, TM-score 1.00

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 P17065
Elsewhere: RCSB PDB 2E7S · PDBe 2E7S · UniProt P17065

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