MolNFT v1 · #108435 · protein

Crystal structure of full-length split GFP mutant D102C disulfide dimer, P 1 space group

4W6R · Fluorescent protein D102C: “Crystal structure of full-length split GFP mutant D102C disulfide dimer, P 1 space group”. X-ray diffraction, 20 pockets (best druggability 0.87). MolNFT v1 #108435 on GenesisL1: 3D structure, binding…

PDB: 4W6R
Type: protein
Length: 3,133 residues
Chains: 16
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fluorescent protein D102C
Pockets: 20 · best druggability 0.87

Structure

x-ray diffraction · 16 distinct chains · 8% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Fluorescent protein D102C	protein	215	9% helix, 43% strand	—
B	Fluorescent protein D102C	protein	205	8% helix, 51% strand	—
C	Fluorescent protein D102C	protein	207	10% helix, 52% strand	—
D	Fluorescent protein D102C	protein	194	11% helix, 39% strand	—
E	Fluorescent protein D102C	protein	208	8% helix, 52% strand	—
F	Fluorescent protein D102C	protein	201	8% helix, 47% strand	—
G	Fluorescent protein D102C	protein	188	4% helix, 54% strand	—
H	Fluorescent protein D102C	protein	191	8% helix, 50% strand	—
I	Fluorescent protein D102C	protein	209	11% helix, 48% strand	—
J	Fluorescent protein D102C	protein	184	5% helix, 52% strand	—
K	Fluorescent protein D102C	protein	175	8% helix, 38% strand	—
L	Fluorescent protein D102C	protein	197	6% helix, 52% strand	—
M	Fluorescent protein D102C	protein	168	6% helix, 51% strand	—
N	Fluorescent protein D102C	protein	174	4% helix, 55% strand	—
O	Fluorescent protein D102C	protein	213	8% helix, 53% strand	—
P	Fluorescent protein D102C	protein	204	10% helix, 50% strand	—

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	691	0.87	0.90	52	empty
2	659	0.83	0.87	75	empty
3	163	0.82	0.97	38	empty
4	193	0.81	0.95	33	empty
5	137	0.81	0.98	30	empty

Interfaces

25 interfaces between chains.

F–P · 901 Å² buried · 11 hydrogen bonds · protein-protein
C–I · 890 Å² buried · 11 hydrogen bonds · protein-protein
H–L · 778 Å² buried · 9 hydrogen bonds · protein-protein
B–D · 731 Å² buried · 8 hydrogen bonds · protein-protein
G–O · 684 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 7 disulfide (disulfide).

Compared structures

4W6R · Crystal Structure of Full-Length Split GFP Mutant D102C Disulfide Dimer, P 1 Space Group · 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 4W6R · PDBe 4W6R

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