MolNFT v1 · #104509 · protein

PDGF-B blocking antibody bound to PDGF-bb

4QCI · Anti-PDGF-bb antibody - light chain: “PDGF-B blocking antibody bound to PDGF-bb”. X-ray diffraction, 12 pockets (best druggability 0.59). MolNFT v1 #104509 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4QCI
Type: protein
Length: 1,015 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Anti-PDGF-bb antibody - light chain; Anti-PDGF-bb antibody - heavy chain…
UniProt: P01127
Pockets: 12 · best druggability 0.59

Structure

x-ray diffraction · 6 distinct chains · 6% helix, 53% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Anti-PDGF-bb antibody - light chain	protein	206	8% helix, 51% strand	—
B	Anti-PDGF-bb antibody - heavy chain	protein	214	6% helix, 51% strand	—
C	Platelet-derived growth factor subunit B	protein	92	4% helix, 61% strand	P01127
D	Platelet-derived growth factor subunit B	protein	96	0% helix, 61% strand	P01127
H	Anti-PDGF-bb antibody - heavy chain	protein	204	6% helix, 52% strand	—
L	Anti-PDGF-bb antibody - light chain	protein	203	8% helix, 51% strand	—

Pockets

12 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	487	0.59	0.74	55	empty
2	465	0.59	0.74	51	empty
3	59	0.55	0.89	20	empty
4	105	0.51	0.82	25	empty
5	121	0.46	0.79	19	empty

Interfaces

9 interfaces between chains.

H–L · 1693 Å² buried · 14 hydrogen bonds · protein-protein
A–B · 1686 Å² buried · 15 hydrogen bonds · protein-protein
C–D · 1067 Å² buried · 9 hydrogen bonds · protein-protein
A–D · 531 Å² buried · 7 hydrogen bonds · protein-protein
B–D · 518 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide (disulfide).

Compared structures

4QCI · PDGF-B blocking antibody bound to PDGF-BB · the same entry in another collection · chain L against L, TM-score 1.00
P01127 · AlphaFold monomer V2.0 prediction for platelet-derived growth factor subunit B (P01127) · a predicted model of the same protein · chain C against A, TM-score 0.93

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 P01127
Elsewhere: RCSB PDB 4QCI · PDBe 4QCI · UniProt P01127

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