4KV5: ScFv GC1009

scFv GC1009 in complex with TGF-beta1. Determined by X-ray diffraction at 3.0 Å resolution. Released 24 Sept 2014.

Method: X-ray diffraction
Resolution: 3.0 Å
Organism: Homo sapiens
Chains: 8
Atoms: 10,542
Mol. weight: 157.87 kDa
Released: 24 Sept 2014

Explore 4KV5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4KV5 contains 37 α-helices and 139 β-strands across 8 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chains A and C: 3 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	9
α-helix	4-8	5
β-strand	16-18	3	10
β-strand	21-23	3	11
α-helix	24-28	5
β-strand	33-35	3	9
β-strand	38-40	3	11
β-strand	43-45	3	10
β-strand	54	1	9
α-helix	57-67	11
β-strand	78-92	15	9
β-strand	95-111	17	9

Chain B: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	12
α-helix	4-8	5
β-strand	16-18	3	13
β-strand	22-23	2	14
α-helix	24-28	5
β-strand	35	1	15
β-strand	38-39	2	14
β-strand	43-45	3	13
β-strand	54	1	16
α-helix	57-67	11
β-strand	78-80	3	16
β-strand	83-92	10	15
β-strand	93	1	17
β-strand	95-106	12	15
β-strand	108	1	12
β-strand	109-111	3	16

Chain D: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	4
α-helix	4-8	5
β-strand	16-18	3	5
β-strand	22-23	2	6
α-helix	24-28	5
β-strand	33-35	3	7
β-strand	38-39	2	6
β-strand	43-45	3	5
β-strand	54	1	8
α-helix	57-67	11
β-strand	78-80	3	8
β-strand	83-92	10	7
β-strand	95-106	12	7
β-strand	108	1	4
β-strand	109-111	3	8

Chain E: 6 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	25
α-helix	7-9	3
β-strand	10-12	3	26
β-strand	18-24	7	25
β-strand	34-39	6	26
β-strand	45-52	8	26
β-strand	57-60	4	26
α-helix	62-64	3
β-strand	65	1	25
β-strand	68-73	6	25
α-helix	74-76	3
β-strand	78-83	6	25
α-helix	88-90	3
β-strand	92-99	8	26
β-strand	107-110	4	26
β-strand	114-118	5	26
β-strand	141-144	4	27
β-strand	147-150	4	26
β-strand	156-162	7	27
β-strand	171-176	6	26
β-strand	183-187	5	26
β-strand	191-192	2	26
α-helix	193	1
β-strand	200-205	6	27
β-strand	208-213	6	27
β-strand	223-228	6	26
α-helix	234	1
β-strand	235-236	2	26
β-strand	240-244	5	26

Chain G: 6 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	28
α-helix	7-9	3
β-strand	10-12	3	29
β-strand	18-24	7	28
α-helix	29-31	3
β-strand	34-39	6	29
β-strand	45-52	8	29
β-strand	57-60	4	29
α-helix	62-64	3
β-strand	65	1	28
β-strand	68-73	6	28
β-strand	78-83	6	28
α-helix	88-90	3
β-strand	92-99	8	29
β-strand	107-110	4	29
β-strand	114-118	5	29
β-strand	141-144	4	30
β-strand	147-150	4	29
β-strand	156-162	7	30
β-strand	171-176	6	29
β-strand	184-187	4	29
β-strand	191-192	2	29
α-helix	193	1
β-strand	200-205	6	30
β-strand	208-213	6	30
β-strand	223-228	6	29
α-helix	234	1
β-strand	235-236	2	29
β-strand	237	1	30
β-strand	240-244	5	29

Chain H: 7 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	21
α-helix	7-9	3
β-strand	10-12	3	22
β-strand	17-24	8	21
α-helix	29-31	3
β-strand	34-39	6	22
β-strand	45-52	8	22
β-strand	57-60	4	22
α-helix	62-64	3
β-strand	65	1	21
β-strand	68-73	6	21
β-strand	78-84	7	21
α-helix	88-90	3
β-strand	92-99	8	22
β-strand	107-110	4	22
β-strand	114-118	5	22
β-strand	141-144	4	23
β-strand	147-150	4	22
β-strand	152	1	24
β-strand	154	1	24
β-strand	156-162	7	23
β-strand	171-176	6	22
β-strand	183-187	5	22
β-strand	191-192	2	22
α-helix	193	1
β-strand	200-205	6	23
β-strand	208-213	6	23
α-helix	218-220	3
β-strand	223-228	6	22
α-helix	234	1
β-strand	235-236	2	22
β-strand	240-244	5	22

Chain J: 6 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	18
α-helix	7-9	3
β-strand	10-12	3	19
β-strand	18-24	7	18
β-strand	34-39	6	19
β-strand	45-52	8	19
β-strand	57-60	4	19
α-helix	62-64	3
β-strand	65	1	18
β-strand	68-73	6	18
β-strand	78-83	6	18
α-helix	88-90	3
β-strand	92-99	8	19
β-strand	107-110	4	19
β-strand	114-118	5	19
β-strand	141-144	4	20
β-strand	147-150	4	19
β-strand	156-162	7	20
β-strand	171-176	6	19
β-strand	183-187	5	19
β-strand	191-192	2	19
α-helix	193	1
β-strand	200-205	6	20
β-strand	208-213	6	20
α-helix	218-220	3
β-strand	223-228	6	19
β-strand	231	1	17
α-helix	234	1
β-strand	235-236	2	19
β-strand	240-244	5	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transforming growth factor beta-1 proprotein	A, B, C, D	protein	112	Homo sapiens	P01137 (AlphaFold model)
Single-chain variable fragment GC1009	E, G, H, J	protein	252	Homo sapiens

Sequence of entity 1 (A, B, C, D), FASTA

>4KV5_1 Transforming growth factor beta-1 proprotein (chains A, B, C, D)
ALDTNYCFSSTEKNCCVRQLYIDFRKDLGWKWIHEPKGYHANFCLGPCPYIWSLDTQYSK
VLALYNQHNPGASAAPCCVPQALEPLPIVYYVGRKPKVEQLSNMIVRSCKCS

Sequence of entity 2 (E, G, H, J), FASTA

>4KV5_2 Single-chain variable fragment GC1009 (chains E, G, H, J)
QVQLVQSGAEVKKPGSSVKVSCKASGYTFSSNVISWVRQAPGQGLEWMGGVIPIVDIANY
AQRFKGRVTITADESTSTTYMELSSLRSEDTAVYYCASTLGLVLDAMDYWGQGTLVTVSS
GGGGSGGGGSGGGGSALETVLTQSPGTLSLSPGERATLSCRASQSLGSSYLAWYQQKPGQ
APRLLIYGASSRAPGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYADSPITFGQGT
RLEIKRHHHHHH

Primary citation

Structures of a pan-specific antagonist antibody complexed to different isoforms of TGF beta reveal structural plasticity of antibody-antigen interactions. Moulin, A., Mathieu, M., Lawrence, C. et al. Protein Sci (2014) 23:1698-1707. DOI 10.1002/pro.2548 · PubMed

Other PDB entries of the same protein (UniProt P01137 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8UDZ 2.21 Å, The Structure of LTBP-49247 Fab Bound to TGFbeta1 Small Latent Complex
9VJJ 2.48 Å, Crystal Structure of human Latent TGF-beta1 in complex with SOF10
8C7H 2.7 Å, Cryo-EM Map of the latTGF-beta LHG-10 Fab complex
13FJ 2.75 Å, TGFB1 in complex with NIS793 FAB
6OM2 2.77 Å, Crystal structure of atypical integrin alphaV beta8 with proTGF-beta1 ligand peptide
5VQP 2.9 Å, Crystal structure of human pro-TGF-beta1
8REW 2.98 Å, CryoEM structure of human GARP-lTGFbeta1 in complex with a Fab fragment derived from an…
3KFD 3.0 Å, Ternary complex of TGF-b1 reveals isoform-specific ligand recognition and receptor…
8VSC 3.0 Å, L-tgf-b1/GARP
9R3S 3.06 Å, pro-TGF-beta1 in complex with the third TB Domain from Latent Transforming Growth…
6GFF 3.1 Å, Structure of GARP (LRRC32) in complex with latent TGF-beta1 and MHG-8 Fab
8VSD 3.2 Å, avb8/L-TGF-b1/GARP

Browse structure collections

About this viewer

MolViewer shows 4KV5 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.