Research workbench

Branchiostoma floridae fluorescent protein LANFP10A2

Analyse Branchiostoma floridae fluorescent protein LANFP10A2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7SFA
Type: protein
Length: 869 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fluorescent protein LANFP10A2
Ligands: JBY
Pockets: 14 · best druggability 0.87

Structure

x-ray diffraction · 4 distinct chains · 10% helix, 56% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Fluorescent protein LANFP10A2	protein	215	10% helix, 57% strand	—
B	Fluorescent protein LANFP10A2	protein	221	10% helix, 56% strand	—
C	Fluorescent protein LANFP10A2	protein	216	10% helix, 57% strand	—
D	Fluorescent protein LANFP10A2	protein	217	10% helix, 56% strand	—

Ligands and binding sites

JBY · (2S)-2-{(4Z)-2-(aminomethyl)-4-[(4-hydroxyphenyl) methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}propanoic acid · ligand · 4 copies · chains A, B, C, D

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

Pockets

14 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	1051	0.87	0.88	110	empty
2	105	0.78	0.98	34	JBY
3	98	0.77	0.98	29	JBY
4	100	0.76	0.97	35	JBY
5	88	0.75	0.97	26	JBY

Interfaces

6 interfaces between chains.

B–C · 1207 Å² buried · 11 hydrogen bonds · protein-protein
A–D · 1198 Å² buried · 10 hydrogen bonds · protein-protein
B–D · 1005 Å² buried · 23 hydrogen bonds · protein-protein
A–C · 986 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 124 Å² buried · 1 hydrogen bond · protein-protein

Modifications

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

Compared structures

7SFA · Branchiostoma floridae fluorescent protein LanFP10A2 · 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
Elsewhere: RCSB PDB 7SFA · PDBe 7SFA

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