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Crystal structure of microcin immunity protein mccf from bacillus anthracis in complex with mcc

Analyse Crystal structure of microcin immunity protein mccf from bacillus anthracis in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5K99
Type: protein
Length: 681 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Microcin C7 self-immunity protein mccf; Microcin C
UniProt: Q81RT8
Ligands: AMP
Pockets: 4 · best druggability 0.80

Structure

x-ray diffraction · 3 distinct chains · 31% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Microcin C7 self-immunity protein mccf	protein	336	31% helix, 22% strand	Q81RT8
C, D	Microcin C	protein	6	0% helix, 0% strand	—
B	Microcin C7 self-immunity protein mccf	protein	333	32% helix, 23% strand	Q81RT8

Ligands and binding sites

AMP · Adenosine monophosphate · ligand · 2 copies · chains A, C, B, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	993	0.80	0.82	109	AMP
2	92	0.40	0.77	22	empty
3	54	0.33	0.77	17	empty
4	57	0.27	0.73	13	empty

Interfaces

6 interfaces between chains.

A–B · 1864 Å² buried · 47 hydrogen bonds · protein-protein
B–D · 306 Å² buried · 8 hydrogen bonds · protein-protein
A–C · 303 Å² buried · 8 hydrogen bonds · protein-protein
A–D · 100 Å² buried · 2 hydrogen bonds · protein-protein
C–B · 93 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 18 modified, 2 covalent (engineered, covalent ligand, nonstandard).

Compared structures

5K99 · Crystal structure of microcin immunity protein MccF from Bacillus anthracis in complex… · 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 Q81RT8
Elsewhere: RCSB PDB 5K99 · PDBe 5K99 · UniProt Q81RT8

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