MolNFT v1 · #108431 · protein

Crystal structure of full-length split GFP mutant D117C disulfide dimer, C 1 2 1 space group

4W6N · Fluorescent protein D117C: “Crystal structure of full-length split GFP mutant D117C disulfide dimer, C 1 2 1 space group”. X-ray diffraction, 1 ligand (CRO), 20 pockets (best druggability 0.84). MolNFT v1 #108431 on GenesisL1: 3D…

PDB: 4W6N
Type: protein
Length: 1,302 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fluorescent protein D117C
Ligands: CRO
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 6 distinct chains · 8% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Fluorescent protein D117C	protein	216	9% helix, 49% strand	—
B	Fluorescent protein D117C	protein	217	8% helix, 52% strand	—
C	Fluorescent protein D117C	protein	218	10% helix, 53% strand	—
D	Fluorescent protein D117C	protein	221	8% helix, 52% strand	—
E	Fluorescent protein D117C	protein	221	10% helix, 53% strand	—
F	Fluorescent protein D117C	protein	209	6% helix, 52% strand	—

Ligands and binding sites

CRO · {2-[(1R,2R)-1-amino-2-hydroxypropyl]-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid · ligand · 4 copies · chains A, B, C, F

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

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	250	0.84	0.95	40	CRO
2	176	0.82	0.96	40	empty
3	157	0.81	0.97	30	empty
4	149	0.81	0.97	27	CRO
5	141	0.79	0.96	29	CRO

Interfaces

9 interfaces between chains.

B–E · 880 Å² buried · 14 hydrogen bonds · protein-protein
C–F · 869 Å² buried · 15 hydrogen bonds · protein-protein
A–C · 446 Å² buried · 9 hydrogen bonds · protein-protein
C–D · 266 Å² buried · 1 hydrogen bond · protein-protein
A–E · 219 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 7 cofactor, 3 disulfide (chromophore, disulfide).

Compared structures

4W6N · Crystal Structure of Full-Length Split GFP Mutant D117C Disulfide Dimer, C 1 2 1 Space… · 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 4W6N · PDBe 4W6N

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