MolNFT v1 · #120974 · protein

Crystal structure of chemically synthesized heterochiral {RFX037 plus VEGF-a} protein complex in space group P21/N

5HHC · Vascular endothelial growth factor a: “Crystal structure of chemically synthesized heterochiral {RFX037 plus VEGF-a} protein complex in space group…”. X-ray diffraction, 3 pockets (best druggability 0.46). MolNFT v1 #120974 on…

PDB: 5HHC
Type: protein
Length: 324 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Vascular endothelial growth factor a; D- vascular endothelial growth factor-a
UniProt: P15692
Pockets: 3 · best druggability 0.46

Structure

x-ray diffraction · 3 distinct chains · 19% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Vascular endothelial growth factor a	protein	95	13% helix, 63% strand	P15692
C	D- vascular endothelial growth factor-a	protein	66	20% helix, 45% strand	—
D	D- vascular endothelial growth factor-a	protein	68	26% helix, 44% strand	—

Ligands and binding sites

GOL · Glycerol · additive · 2 copies · chains A, B

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

Pockets

3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	204	0.46	0.74	45	GOL
2	61	0.26	0.72	14	empty
3	53	0.26	0.73	14	empty

Interfaces

5 interfaces between chains.

A–B · 1393 Å² buried · 12 hydrogen bonds · protein-protein
A–D · 390 Å² buried · 8 hydrogen bonds · protein-protein
A–C · 362 Å² buried · 1 hydrogen bond · protein-protein
B–C · 362 Å² buried · 5 hydrogen bonds · protein-protein
B–D · 357 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 122 d-amino, 8 disulfide (D-amino acid, disulfide).

Compared structures

5HHC · Crystal Structure of Chemically Synthesized Heterochiral {RFX037 plus VEGF-A} Protein… · 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
Every structure of UniProt P15692
Elsewhere: RCSB PDB 5HHC · PDBe 5HHC · UniProt P15692

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