MolNFT v1 · #82443 · protein

Crystal structure of tryptophan synthase alpha-subunit from the psychrophile shewanella frigidimarina K14-2

3VND · Tryptophan synthase alpha chain: “Crystal structure of tryptophan synthase alpha-subunit from the psychrophile shewanella frigidimarina K14-2”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.84). MolNFT v1 #82443…

PDB: 3VND
Type: protein
Length: 2,072 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tryptophan synthase alpha chain
EC: 4.2.1.20
UniProt: H1AFK5
Ligands: SO4
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 1 distinct chain · 53% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H	Tryptophan synthase alpha chain (EC 4.2.1.20)	protein	259	53% helix, 14% strand	H1AFK5

Ligands and binding sites

SO4 · Sulfate ion · ion · 18 copies · chains A, B, C, D, E, F, G, H
PE8 · 3,6,9,12,15,18,21-heptaoxatricosane-1,23-diol · additive · 4 copies · chains A, B, C, D, E, F, G, H

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

Pockets

20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1044	0.84	0.85	96	SO4, PE8
2	1007	0.84	0.84	96	SO4, PE8
3	1194	0.82	0.83	106	SO4, PE8
4	1176	0.82	0.83	102	SO4, PE8
5	677	0.77	0.82	51	SO4

Interfaces

10 interfaces between chains.

E–F · 969 Å² buried · 18 hydrogen bonds · protein-protein
G–H · 946 Å² buried · 19 hydrogen bonds · protein-protein
A–B · 928 Å² buried · 19 hydrogen bonds · protein-protein
C–D · 926 Å² buried · 21 hydrogen bonds · protein-protein
B–F · 425 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

3VND · Crystal structure of tryptophan synthase alpha-subunit from the psychrophile Shewanella… · the same entry in another collection · chain A against A, 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 H1AFK5
Elsewhere: RCSB PDB 3VND · PDBe 3VND · UniProt H1AFK5

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