MolNFT v1 · #156826 · protein

X-ray structure of monomeric near-infrared fluorescent protein MIRFP670NANO

6MGH: “X-ray structure of monomeric near-infrared fluorescent protein MIRFP670NANO”. X-ray diffraction, 1 ligand (JRA), 18 pockets (best druggability 0.80). MolNFT v1 #156826 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6MGH
Type: protein
Length: 1,188 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MIRFP670NANO
Ligands: JRA
Pockets: 18 · best druggability 0.80

Structure

x-ray diffraction · 7 distinct chains · 38% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	MIRFP670NANO	protein	147	37% helix, 27% strand	—
B	MIRFP670NANO	protein	146	37% helix, 27% strand	—
C	MIRFP670NANO	protein	145	37% helix, 27% strand	—
D, G	MIRFP670NANO	protein	152	40% helix, 26% strand	—
E	MIRFP670NANO	protein	149	39% helix, 26% strand	—
F	MIRFP670NANO	protein	146	37% helix, 27% strand	—
H	MIRFP670NANO	protein	151	41% helix, 29% strand	—

Ligands and binding sites

JRA · 3-[2-[(~{Z})-[5-[(~{Z})-[(3~{S},4~{R})-3-ethenyl-4-methyl-5-oxidanylidene-pyrrolidin-2-ylidene]methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-pyrrol-2-ylidene]methyl]-5-[(~{Z})-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-4-methyl-1~{H}-pyrrol-3-yl]propanoic acid · ligand · 8 copies · chains A, B, C, F, D, E, G, H
GOL · Glycerol · additive · 4 copies · chains B, C, G, H
IPA · Isopropyl alcohol · additive · 2 copies · chains B, A, C

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

Pockets

18 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	617	0.80	0.85	66	JRA
2	401	0.73	0.83	45	JRA
3	164	0.71	0.89	25	JRA
4	196	0.70	0.87	27	JRA
5	171	0.70	0.88	28	JRA

Interfaces

8 interfaces between chains.

F–G · 1040 Å² buried · 5 hydrogen bonds · protein-protein
A–H · 1014 Å² buried · 8 hydrogen bonds · protein-protein
B–D · 999 Å² buried · 9 hydrogen bonds · protein-protein
C–E · 980 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 919 Å² buried · 23 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 covalent (covalent ligand).

Compared structures

6MGH · X-ray structure of monomeric near-infrared fluorescent protein miRFP670nano · the same entry in another collection · chain G against G, 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 6MGH · PDBe 6MGH

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