MolNFT v1 · #97972 · protein

Scfv GC1009 in complex with TGF-BETA1.

4KV5 · Transforming growth factor beta-1 proprotein: “Scfv GC1009 in complex with TGF-BETA1.”. X-ray diffraction, 15 pockets (best druggability 0.69). MolNFT v1 #97972 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4KV5
Type: protein
Length: 1,366 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transforming growth factor beta-1 proprotein; Single-chain variable fragment GC1009
UniProt: P01137
Pockets: 15 · best druggability 0.69

Structure

x-ray diffraction · 4 distinct chains · 6% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C, D, A, B	Transforming growth factor beta-1 proprotein	protein	112	19% helix, 44% strand	P01137
J, E	Single-chain variable fragment GC1009	protein	230	4% helix, 50% strand	—
H	Single-chain variable fragment GC1009	protein	229	5% helix, 51% strand	—
G	Single-chain variable fragment GC1009	protein	229	4% helix, 50% strand	—

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	651	0.69	0.77	54	empty
2	231	0.49	0.74	30	empty
3	60	0.47	0.84	15	empty
4	69	0.40	0.80	19	empty
5	78	0.38	0.77	19	empty

Interfaces

12 interfaces between chains.

A–B · 1368 Å² buried · 10 hydrogen bonds · protein-protein
C–D · 1336 Å² buried · 9 hydrogen bonds · protein-protein
D–G · 708 Å² buried · 6 hydrogen bonds · protein-protein
B–J · 693 Å² buried · 4 hydrogen bonds · protein-protein
A–H · 692 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 26 disulfide (disulfide).

Compared structures

4KV5 · scFv GC1009 in complex with TGF-beta1. · the same entry in another collection · chain G against G, TM-score 1.00
P01137 · AlphaFold monomer V2.0 prediction for transforming growth factor beta-1 proprotein… · a predicted model of the same protein · chain C against A, TM-score 0.81

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 P01137
Elsewhere: RCSB PDB 4KV5 · PDBe 4KV5 · UniProt P01137

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