MolNFT v1 · #109587 · protein

Crystal structure of saga-2006 GII.4 P domain in complex with nano-85

4X7C · VP1: “Crystal structure of saga-2006 GII.4 P domain in complex with nano-85”. X-ray diffraction, 8 pockets (best druggability 0.70). MolNFT v1 #109587 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4X7C
Type: protein
Length: 850 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: VP1; Nano-85 nanobody
UniProt: B5BTR4
Pockets: 8 · best druggability 0.70

Structure

x-ray diffraction · 3 distinct chains · 5% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	VP1	protein	307	5% helix, 36% strand	B5BTR4
C	Nano-85 nanobody	protein	116	5% helix, 58% strand	—
D	Nano-85 nanobody	protein	120	5% helix, 56% strand	—

Pockets

8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	50	0.70	0.98	19	empty
2	478	0.68	0.79	52	empty
3	431	0.67	0.80	51	empty
4	173	0.55	0.80	36	empty
5	59	0.41	0.81	15	empty

Interfaces

3 interfaces between chains.

A–B · 1807 Å² buried · 18 hydrogen bonds · protein-protein
B–D · 801 Å² buried · 7 hydrogen bonds · protein-protein
A–C · 770 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

4X7C · Crystal structure of Saga-2006 GII.4 P domain in complex with Nano-85 · the same entry in another collection · chain C against C, 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 B5BTR4
Elsewhere: RCSB PDB 4X7C · PDBe 4X7C · UniProt B5BTR4

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