7QOT: Coagulation factor XIa heavy chain

Factor XI and Plasma Kallikrein apple domain structures reveals different kininogen bound complexes. Determined by X-ray diffraction at 3.24 Å resolution. Released 18 Jan 2023.

Method: X-ray diffraction
Resolution: 3.24 Å
Organism: Homo sapiens
Chains: 4
Atoms: 5,910
Mol. weight: 88.08 kDa
Ligands: NAG
Released: 18 Jan 2023

Explore 7QOT in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7QOT contains 16 α-helices and 55 β-strands across 4 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: 7 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	7	1	1
β-strand	10-12	3	2
β-strand	16-21	6	1
α-helix	25-34	10
β-strand	40-44	5	1
α-helix	52-54	3
β-strand	57-61	5	1
β-strand	70-72	3	2
β-strand	76-80	5	1
β-strand	96-98	3	3
β-strand	101-103	3	4
β-strand	105-111	7	3
α-helix	115-124	10
β-strand	130-134	5	3
β-strand	146-151	6	3
β-strand	159-161	3	4
β-strand	166-170	5	3
α-helix	173-175	3
β-strand	186-187	2	5
β-strand	191-192	2	6
β-strand	195-201	7	5
α-helix	205-214	10
β-strand	220-224	5	5
α-helix	231-233	3
β-strand	236-241	6	5
β-strand	250-251	2	6
β-strand	256-260	5	5
β-strand	278-283	6	7
β-strand	286-293	8	7
α-helix	296-305	10
β-strand	311-315	5	7
β-strand	326-332	7	7
β-strand	341-351	11	7

Chain B: 8 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	7	1	8
β-strand	10-12	3	9
β-strand	16-21	6	8
α-helix	25-34	10
β-strand	40-44	5	8
α-helix	52-54	3
β-strand	57-61	5	8
β-strand	70-72	3	9
β-strand	76-80	5	8
α-helix	95	1
β-strand	96-98	3	10
β-strand	101-102	2	11
β-strand	108-111	4	10
α-helix	115-124	10
β-strand	130-134	5	10
β-strand	146-150	5	10
β-strand	160-161	2	11
β-strand	166-170	5	10
β-strand	183-187	5	12
β-strand	191	1	13
β-strand	195-201	7	12
α-helix	205-214	10
β-strand	220-224	5	12
α-helix	231-233	3
β-strand	236-241	6	12
β-strand	251	1	13
β-strand	256-261	6	12
α-helix	268-272	5
β-strand	278	1	7
β-strand	281-283	3	14
β-strand	286-293	8	7
α-helix	296-305	10
β-strand	311-315	5	7
β-strand	326-332	7	7
β-strand	341-343	3	14
β-strand	348-351	4	7

Chain C: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	577	1	5

Chain D: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	583-586	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Coagulation factor XIa heavy chain	A, B	protein	358	Homo sapiens	P03951 (AlphaFold model)
Kininogen-1 light chain	C, D	protein	31	Homo sapiens	P01042 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>7QOT_1 Coagulation factor XIa heavy chain (chains A, B)
ECVTQLLKDTCFEGGDITTVFTPSAKYCQVVCTYHPRCLLFTFTAESPSEDPTRWFTCVL
KDSVTETLPRVNRTAAISGYSFKQCSHQISACNKDIYVDLDMKGINYNSSVAKSAQECQE
RCTDDVHCHFFTYATRQFPSLEHRNICLLKHTQTGTPTRITKLDKVVSGFSLKSCALSNL
ACIRDIFPNTVFADSNIDSVMAPDAFVCGRICTHHPGCLFFTFFSQEWPKESQRNLCLLK
TSESGLPSTRIKKSKALSGFSLQSCRHSIPVFCHSSFYHDTDFLGEELDIVAAKSHEACQ
KLCTNAVRCQFFTYTPAQASCNEGKGKCYLKLSSNGSPTKILHGRGGISGYTLRLCKM

Sequence of entity 2 (C, D), FASTA

>7QOT_2 Kininogen-1 light chain (chains C, D)
SDDDWIPDIQIDPNGLSFNPISDFPDTTSPK

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	3

Water and common crystallization additives (SO4) are not listed.

Primary citation

Plasma kallikrein structure reveals apple domain disc rotated conformation compared to factor XI. Li, C., Voos, K.M., Pathak, M. et al. J Thromb Haemost (2019) 17:759-770. DOI 10.1111/jth.14418 · PubMed

Other PDB entries of the same protein (UniProt P03951 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7MBO 0.92 Å, FACTOR XIA (PICHIA PASTORIS; C500S [C122S]) IN COMPLEX WITH THE INHIBITOR Milvexian…
6TS4 1.17 Å, Coagulation factor XI protease domain in complex with active site inhibitor
4CRG 1.25 Å, Creating novel F1 inhibitors through fragment based lead generation and structure aided…
8BO6 1.25 Å, Coagulation factor XI protease domain in complex with active site inhibitor 2
8BO7 1.25 Å, Coagulation factor XI protease domain in complex with active site inhibitor 34
6USY 1.26 Å, Coagulation factor XI catalytic domain (C123S) in complex with nvp-XIV936
6TS5 1.29 Å, Coagulation factor XI protease domain in complex with active site inhibitor
6TS6 1.33 Å, Coagulation factor XI protease domain in complex with active site inhibitor
7V11 1.47 Å, Factor XIa in Complex with Compound 2e
5EXN 1.49 Å, FACTOR XIA (C500S [C122S]) IN COMPLEX WITH THE INHIBITOR methyl…
7V16 1.5 Å, Factor XIa in Complex with Compound 2j
7V17 1.52 Å, Factor XIa in Complex with Compound 2k

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