MolNFT v1 · #144677 · protein

Lysinoalanine synthase, durn, from duramycin biosynthesis bound to duramycin

6C0Y: “Lysinoalanine synthase, durn, from duramycin biosynthesis bound to duramycin”. X-ray diffraction, 1 ligand (K), 10 pockets (best druggability 0.74). MolNFT v1 #144677 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6C0Y
Type: protein
Length: 1,009 residues
Chains: 16
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lysinoalanine synthase; Cys-lys-gln-dal-cys-ala-phe-gly-pro-phe-dbb-phe-val-cys…
Ligands: K
Pockets: 10 · best druggability 0.74

Structure

x-ray diffraction · 5 distinct chains · 54% helix, 7% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Lysinoalanine synthase	protein	107	67% helix, 7% strand	—
C, D, E, F, G, H	Lysinoalanine synthase	protein	108	67% helix, 6% strand	—
O, I, J, K, N, P	Cys-lys-gln-dal-cys-ala-phe-gly-pro-phe-dbb-phe-val-cys- BH2-gly-asn-dbb-lys	protein	19	0% helix, 21% strand	—
L	Cys-lys-gln-dal-cys-ala-phe-gly-pro-phe-dbb-phe-val-cys- BH2-gly-asn-dbb-lys	protein	18	0% helix, 11% strand	—
M	Cys-lys-gln-dal-cys-ala-phe-gly-pro-phe-dbb-phe-val-cys- BH2-gly-asn-dbb-lys	protein	15	0% helix, 0% strand	—

Ligands and binding sites

K · Potassium ion · metal · 8 copies · chains A, E, B, F, C, G, D, H

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

Pockets

10 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	587	0.74	0.82	67	empty
2	831	0.73	0.78	68	empty
3	610	0.72	0.79	62	empty
4	599	0.68	0.77	53	empty
5	106	0.44	0.79	19	empty

Interfaces

37 interfaces between chains.

C–G · 3277 Å² buried · 45 hydrogen bonds · protein-protein
D–H · 3256 Å² buried · 44 hydrogen bonds · protein-protein
A–E · 3219 Å² buried · 45 hydrogen bonds · protein-protein
B–F · 3196 Å² buried · 43 hydrogen bonds · protein-protein
C–O · 604 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 23 modified, 8 d-amino (nonstandard, D-amino acid).

Compared structures

6C0Y · Lysinoalanine synthase, DurN, from duramycin biosynthesis bound to duramycin · 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
Elsewhere: RCSB PDB 6C0Y · PDBe 6C0Y

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