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Crystal structure of the putative nitroreductase (SMU.260) in complex with FMN from streptococcus mutans, northeast structural genomics target SMR5.

Analyse Crystal structure of the putative nitroreductase (SMU.260) in complex with FMN… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2IFA
Type: protein
Length: 1,202 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hypothetical protein SMU.260
UniProt: Q8DW21
Ligands: FMN
Pockets: 8 · best druggability 0.87

Structure

x-ray diffraction · 3 distinct chains · 50% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Hypothetical protein SMU.260	protein	200	50% helix, 19% strand	Q8DW21
B, C, E	Hypothetical protein SMU.260	protein	201	51% helix, 18% strand	Q8DW21
F	Hypothetical protein SMU.260	protein	199	48% helix, 19% strand	Q8DW21

Ligands and binding sites

FMN · Flavin mononucleotide · ligand · 6 copies · chains A, B, C, D, F, E

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

Pockets

8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1152	0.87	0.89	126	FMN
2	1113	0.87	0.88	104	FMN
3	258	0.66	0.83	24	empty
4	316	0.63	0.80	38	FMN
5	319	0.62	0.79	38	FMN

Interfaces

11 interfaces between chains.

C–D · 3262 Å² buried · 43 hydrogen bonds · protein-protein
A–B · 3252 Å² buried · 40 hydrogen bonds · protein-protein
E–F · 3165 Å² buried · 39 hydrogen bonds · protein-protein
C–F · 509 Å² buried · 4 hydrogen bonds · protein-protein
D–F · 428 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 18 modified (engineered).

Compared structures

2IFA · Crystal Structure of the PUTATIVE NITROREDUCTASE (SMU.260) IN COMPLEX WITH FMN FROM… · 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 Q8DW21
Elsewhere: RCSB PDB 2IFA · PDBe 2IFA · UniProt Q8DW21

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