MolNFT v1 · #73912 · protein

Structure of the GFP:GFP-nanobody complex at 2.8 a resolution in spacegroup P21212

3OGO · Green fluorescent protein: “Structure of the GFP:GFP-nanobody complex at 2.8 a resolution in spacegroup P21212”. X-ray diffraction, 1 ligand (CRO), 19 pockets (best druggability 0.79). MolNFT v1 #73912 on GenesisL1: 3D structure…

PDB: 3OGO
Type: protein
Length: 1,369 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Green fluorescent protein; GFP-nanobody
UniProt: P42212
Ligands: CRO
Pockets: 19 · best druggability 0.79

Structure

x-ray diffraction · 7 distinct chains · 9% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Green fluorescent protein	protein	231	12% helix, 50% strand	P42212
B	Green fluorescent protein	protein	224	13% helix, 52% strand	P42212
C	Green fluorescent protein	protein	227	11% helix, 51% strand	P42212
D	Green fluorescent protein	protein	225	11% helix, 52% strand	P42212
E, F	GFP-nanobody	protein	115	3% helix, 50% strand	—
G	GFP-nanobody	protein	116	5% helix, 51% strand	—
H	GFP-nanobody	protein	116	3% helix, 51% 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, D
IPA · Isopropyl alcohol · additive · 3 copies · chains A, E, D, F, C

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

Pockets

19 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	110	0.79	0.98	27	CRO
2	101	0.79	0.99	31	CRO
3	96	0.77	0.98	27	CRO
4	101	0.76	0.97	27	CRO
5	679	0.71	0.78	83	IPA

Interfaces

14 interfaces between chains.

C–F · 718 Å² buried · 18 hydrogen bonds · protein-protein
B–G · 714 Å² buried · 17 hydrogen bonds · protein-protein
E–F · 690 Å² buried · 11 hydrogen bonds · protein-protein
C–H · 382 Å² buried · 7 hydrogen bonds · protein-protein
B–C · 377 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

3OGO · Structure of the GFP:GFP-nanobody complex at 2.8 A resolution in spacegroup P21212 · the same entry in another collection · chain H against H, TM-score 1.00
P42212 · AlphaFold monomer V2.0 prediction for green fluorescent protein (P42212) · a predicted model of the same protein · chain B 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 P42212
Elsewhere: RCSB PDB 3OGO · PDBe 3OGO · UniProt P42212

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