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Serine dehydratase like-1 from human cancer cells

Analyse Serine dehydratase like-1 from human cancer cells in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2RKB
Type: protein
Length: 1,590 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Serine dehydratase-like
EC: 4.3.1.-
UniProt: Q96GA7
Ligands: PLP, K
Pockets: 11 · best druggability 0.86

Structure

x-ray diffraction · 1 distinct chain · 47% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E	Serine dehydratase-like (EC 4.3.1.-)	protein	318	47% helix, 17% strand	Q96GA7

Ligands and binding sites

PLP · Pyridoxal-5'-phosphate · ligand · 5 copies · chains A, B, C, D, E
K · Potassium ion · metal · 5 copies · chains A, B, C, D, E

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

Pockets

11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1162	0.86	0.87	168	PLP
2	930	0.78	0.80	100	PLP
3	945	0.76	0.79	99	PLP
4	610	0.70	0.79	55	PLP
5	162	0.57	0.82	23	empty

Interfaces

8 interfaces between chains.

A–B · 1133 Å² buried · 16 hydrogen bonds · protein-protein
C–D · 1090 Å² buried · 14 hydrogen bonds · protein-protein
A–D · 803 Å² buried · 14 hydrogen bonds · protein-protein
B–C · 779 Å² buried · 10 hydrogen bonds · protein-protein
A–E · 748 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 cofactor (pyridoxal phosphate Schiff base).

Compared structures

2RKB · Serine dehydratase like-1 from human cancer cells · the same entry in another collection · chain A against A, TM-score 1.00
Q96GA7 · AlphaFold monomer V2.0 prediction for serine dehydratase-like (Q96GA7) · a predicted model of the same protein · chain A 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 Q96GA7
Elsewhere: RCSB PDB 2RKB · PDBe 2RKB · UniProt Q96GA7

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