4OGY: Fab DX-2930

Crystal structure of Fab DX-2930 in complex with human plasma kallikrein at 2.1 Angstrom resolution. Determined by X-ray diffraction at 2.1 Å resolution. Released 9 Jul 2014.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Homo sapiens
Chains: 6
Atoms: 11,073
Mol. weight: 149.45 kDa
Released: 9 Jul 2014

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

Secondary structure: helices and β-sheets

4OGY contains 52 α-helices and 134 β-strands across 6 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.

Chain A: 11 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	392	1	1
β-strand	395-396	2	2
β-strand	405-411	7	3
β-strand	415-425	11	3
β-strand	428-431	4	3
α-helix	433-436	4
α-helix	442-444	3
β-strand	445-448	4	3
β-strand	453	1	4
α-helix	454-456	3
β-strand	464	1	3
β-strand	466-471	6	3
β-strand	485-489	5	3
α-helix	492-495	4
β-strand	496	1	5
β-strand	499	1	5
α-helix	501-502	2
β-strand	503	1	2
α-helix	504-506	3
α-helix	507-509	3
β-strand	517-521	5	2
β-strand	534	1	4
α-helix	535	1
β-strand	536-539	4	2
β-strand	542-543	2	2
α-helix	545-550	6
β-strand	561-564	4	2
β-strand	572	1	1
β-strand	581-586	6	2
β-strand	589-598	10	2
β-strand	599	1	6
β-strand	609-613	5	2
α-helix	614-617	4
α-helix	618-628	11

Chain B: 11 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	392	1	7
β-strand	395-396	2	8
β-strand	405-411	7	9
β-strand	415-425	11	9
β-strand	428-431	4	9
α-helix	433-436	4
α-helix	442-444	3
β-strand	445-449	5	9
β-strand	453	1	10
α-helix	454-456	3
β-strand	464	1	9
β-strand	466-471	6	9
β-strand	485-489	5	9
α-helix	492-495	4
β-strand	496	1	11
β-strand	499	1	11
α-helix	501-502	2
β-strand	503	1	8
α-helix	504	1
α-helix	507-511	5
β-strand	517-521	5	8
β-strand	534	1	10
α-helix	535	1
β-strand	536-539	4	8
β-strand	542-543	2	8
α-helix	545-550	6
β-strand	561-564	4	8
β-strand	572	1	7
β-strand	581-586	6	8
β-strand	589-598	10	8
β-strand	599	1	12
β-strand	609-613	5	8
α-helix	614-617	4
α-helix	618-628	11

Chain H: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	13
β-strand	10-12	3	14
β-strand	18-25	8	13
β-strand	32-39	8	14
β-strand	45-51	7	14
β-strand	58-60	3	14
β-strand	68-73	6	13
β-strand	78-83	6	13
α-helix	88-90	3
β-strand	92-100	9	14
β-strand	105	1	6
β-strand	110-112	3	14
β-strand	116-120	5	14
α-helix	123-125	3
β-strand	126	1	15
α-helix	127-128	2
β-strand	129-133	5	16
α-helix	134-136	3
β-strand	144-154	11	16
β-strand	155	1	15
β-strand	160-163	4	17
α-helix	164-166	3
β-strand	168	1	17
β-strand	172-174	3	16
α-helix	175-177	3
β-strand	178-179	2	16
β-strand	185-194	10	16
α-helix	195-197	3
β-strand	204-209	6	17
α-helix	210-212	3
β-strand	214-219	6	17

Chains L and N: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	18
β-strand	10-13	4	19
β-strand	19-25	7	18
β-strand	33-38	6	19
β-strand	45-49	5	19
β-strand	53-54	2	19
α-helix	55	1
β-strand	62-67	6	18
β-strand	70-75	6	18
α-helix	80-82	3
β-strand	84-90	7	19
β-strand	96-97	2	19
β-strand	101-105	5	19
β-strand	110	1	20
α-helix	111-112	2
β-strand	113-117	5	21
α-helix	118-120	3
α-helix	121-125	5
β-strand	128-138	11	21
β-strand	139	1	20
β-strand	144-149	6	22
β-strand	152-153	2	22
α-helix	154	1
β-strand	158-162	5	21
α-helix	163-166	4
β-strand	172-181	10	21
α-helix	182-186	5
β-strand	190-196	7	22
β-strand	204-209	6	22

Chain M: 6 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	23
β-strand	10-12	3	24
β-strand	18-25	8	23
β-strand	32-39	8	24
β-strand	45-51	7	24
β-strand	58-60	3	24
β-strand	68-73	6	23
β-strand	78-83	6	23
α-helix	88-90	3
β-strand	92-100	9	24
β-strand	105	1	12
β-strand	110-112	3	24
β-strand	116-120	5	24
α-helix	123-125	3
β-strand	126	1	25
α-helix	127-128	2
β-strand	129-133	5	26
β-strand	146-154	9	26
β-strand	155	1	25
β-strand	160-163	4	27
α-helix	164-166	3
β-strand	168	1	27
β-strand	172-174	3	26
α-helix	175-177	3
β-strand	178-179	2	26
β-strand	185-192	8	26
β-strand	204-209	6	27
α-helix	210-212	3
β-strand	214-219	6	27

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Plasma kallikrein	A, B	protein	241	Homo sapiens	P03952 (AlphaFold model)
Dx-2930 heavy chain	H, M	protein	225	Homo sapiens	S6C4R2 (AlphaFold model)
Dx-2930 light chain	L, N	protein	213	Homo sapiens	Q7Z3Y4 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4OGY_1 Plasma kallikrein (chains A, B)
IVGGTESSWGEWPWQVSLQVKLTAQRHLCGGSLIGHQWVLTAAHCFDGLPLQDVWRIYSG
ILELSDITKDTPFSQIKEIIIHQNYKVSEGNHDIALIKLQAPLEYTEFQKPISLPSKGDT
STIYTNCWVTGWGFSKEKGEIQNILQKVNIPLVTNEECQKRYQDYKITQRMVCAGYKEGG
KDACKGDSGGPLVCKHNGMWRLVGITSWGEGCARREQPGVYTKVAEYMDWILEKTQSSDG
K

Sequence of entity 2 (H, M), FASTA

>4OGY_2 DX-2930 HEAVY CHAIN (chains H, M)
EVQLLESGGGLVQPGGSLRLSCAASGFTFSHYIMMWVRQAPGKGLEWVSGIYSSGGITVY
ADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAYRRIGVPRRDEFDIWGQGTMVTV
SSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQ
SSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSC

Sequence of entity 3 (L, N), FASTA

>4OGY_3 DX-2930 LIGHT CHAIN (chains L, N)
DIQMTQSPSTLSASVGDRVTITCRASQSISSWLAWYQQKPGKAPKLLIYKASTLESGVPS
RFSGSGSGTEFTLTISSLQPDDFATYYCQQYNTYWTFGQGTKVEIKRTVAAPSVFIFPPS
DEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTL
SKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Primary citation

Inhibition of plasma kallikrein by a highly specific active site blocking antibody. Kenniston, J.A., Faucette, R.R., Martik, D. et al. J Biol Chem (2014) 289:23596-23608. DOI 10.1074/jbc.M114.569061 · PubMed

Other PDB entries of the same protein (UniProt P03952 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6I44 1.36 Å, Allosteric activation of human prekallikrein by apple domain disc rotation
2ANY 1.4 Å, Expression, Crystallization and the Three-dimensional Structure of the Catalytic Domain…
5TJX 1.41 Å, Structure of human plasma kallikrein
6T7P 1.42 Å, human plasmakallikrein protease domain in complex with active site directed inhibitor
5F8Z 1.5 Å, The crystal structure of human Plasma Kallikrein in complex with its peptide inhibitor…
5F8X 1.55 Å, The crystal structure of human plasma kallikrein in complex with its peptide inhibitor…
10LR 1.58 Å, N-Alkyl & N-Aryl Aminopyrazole Spirocarbamates: A Two-Pronged Lead Optimization Strategy…
10MW 1.62 Å, N-Alkyl & N-Aryl Aminopyrazole Spirocarbamates: A Two-Pronged Lead Optimization Strategy…
10MV 1.66 Å, N-Alkyl & N-Aryl Aminopyrazole Spirocarbamates: A Two-Pronged Lead Optimization Strategy…
6O1S 1.7 Å, Structure of human plasma kallikrein protease domain with inhibitor
10QS 1.73 Å, N-Alkyl & N-Aryl Aminopyrazole Spirocarbamates: A Two-Pronged Lead Optimization Strategy…
5F8T 1.75 Å, The crystal structure of human Plasma Kallikrein in complex with its peptide inhibitor…

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