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Pyridine synthase, tbtd, from thiomuracin biosynthesis bound to an N- terminal leader peptide fragment

Analyse Pyridine synthase, tbtd, from thiomuracin biosynthesis bound to an N- terminal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5WA4
Type: protein
Length: 1,914 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pyridine synthase tbtd; Tbta 16-mer peptide
UniProt: D6Y504, D6Y501
Pockets: 18 · best druggability 0.83

Structure

x-ray diffraction · 9 distinct chains · 62% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pyridine synthase tbtd	protein	310	61% helix, 9% strand	D6Y504
B	Pyridine synthase tbtd	protein	307	62% helix, 9% strand	D6Y504
C	Pyridine synthase tbtd	protein	308	63% helix, 9% strand	D6Y504
D	Pyridine synthase tbtd	protein	309	63% helix, 9% strand	D6Y504
E	Pyridine synthase tbtd	protein	313	65% helix, 9% strand	D6Y504
F	Pyridine synthase tbtd	protein	308	65% helix, 7% strand	D6Y504
M, O, R	Tbta 16-mer peptide	protein	11	0% helix, 0% strand	D6Y501
N, P	Tbta 16-mer peptide	protein	9	0% helix, 0% strand	D6Y501
Q	Tbta 16-mer peptide	protein	8	0% helix, 0% strand	D6Y501

Pockets

18 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1002	0.83	0.84	98	empty
2	948	0.82	0.83	87	empty
3	1172	0.80	0.81	88	empty
4	1005	0.75	0.77	84	empty
5	970	0.74	0.77	67	empty

Interfaces

21 interfaces between chains.

A–C · 1015 Å² buried · 22 hydrogen bonds · protein-protein
A–D · 1001 Å² buried · 7 hydrogen bonds · protein-protein
B–D · 981 Å² buried · 23 hydrogen bonds · protein-protein
B–F · 953 Å² buried · 9 hydrogen bonds · protein-protein
C–E · 875 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

5WA4 · Pyridine synthase, TbtD, from thiomuracin biosynthesis bound to an N-terminal leader… · 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 D6Y504
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Elsewhere: RCSB PDB 5WA4 · PDBe 5WA4 · UniProt D6Y504 · UniProt D6Y501

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