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Crystal structure of macrocyclase mdnc bound with precursor peptide mdna from microcystis aeruginosa mrc

Analyse Crystal structure of macrocyclase mdnc bound with precursor peptide mdna from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5IG9
Type: protein
Length: 2,575 residues
Chains: 16
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ATP grasp ligase; Microviridin
UniProt: B2G3D0, B2G3C8
Pockets: 20 · best druggability 0.79

Structure

x-ray diffraction · 11 distinct chains · 33% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	ATP grasp ligase	protein	319	32% helix, 27% strand	B2G3D0
B	ATP grasp ligase	protein	305	33% helix, 28% strand	B2G3D0
C	ATP grasp ligase	protein	312	32% helix, 27% strand	B2G3D0
D	ATP grasp ligase	protein	306	33% helix, 29% strand	B2G3D0
E	ATP grasp ligase	protein	312	32% helix, 27% strand	B2G3D0
F	ATP grasp ligase	protein	302	33% helix, 29% strand	B2G3D0
G	ATP grasp ligase	protein	313	32% helix, 27% strand	B2G3D0
H	ATP grasp ligase	protein	310	33% helix, 28% strand	B2G3D0
P, I, J, K, L, O	Microviridin	protein	12	33% helix, 0% strand	B2G3C8
M	Microviridin	protein	11	45% helix, 0% strand	B2G3C8
N	Microviridin	protein	13	38% helix, 0% strand	B2G3C8

Pockets

20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	881	0.79	0.81	90	empty
2	849	0.77	0.80	93	empty
3	614	0.74	0.81	71	empty
4	590	0.74	0.81	54	empty
5	208	0.62	0.82	26	empty

Interfaces

28 interfaces between chains.

C–D · 3033 Å² buried · 53 hydrogen bonds · protein-protein
E–H · 2959 Å² buried · 50 hydrogen bonds · protein-protein
F–G · 2934 Å² buried · 51 hydrogen bonds · protein-protein
A–B · 2914 Å² buried · 50 hydrogen bonds · protein-protein
A–H · 1344 Å² buried · 22 hydrogen bonds · protein-protein

Compared structures

5IG9 · Crystal structure of macrocyclase MdnC bound with precursor peptide MdnA from Microcystis… · 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 B2G3D0
Every structure of UniProt B2G3C8
Elsewhere: RCSB PDB 5IG9 · PDBe 5IG9 · UniProt B2G3D0 · UniProt B2G3C8

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