MolNFT v1 · #122136 · protein

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

5IG9 · ATP grasp ligase: “Crystal structure of macrocyclase mdnc bound with precursor peptide mdna from microcystis aeruginosa mrc”. X-ray diffraction, 20 pockets (best druggability 0.79). MolNFT v1 #122136 on GenesisL1: 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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