5I25: Human recombinant coagulation FXI

human recombinant coagulation FXI in complex with a peptide derived from human high molecular weight kininogen (HKP). Determined by X-ray diffraction at 2.85 Å resolution. Released 6 Apr 2016.

Method: X-ray diffraction
Resolution: 2.85 Å
Organism: Homo sapiens
Chains: 2
Atoms: 4,842
Mol. weight: 69.68 kDa
Ligands: NAG
Released: 6 Apr 2016

Explore 5I25 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5I25 contains 25 α-helices and 42 β-strands across 2 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: 24 helices, 42 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	96-102	7	3
β-strand	105-111	7	3
α-helix	115-124	10
β-strand	130-134	5	3
α-helix	141-143	3
β-strand	146-151	6	3
β-strand	160-170	11	3
α-helix	173-175	3
α-helix	180-182	3
β-strand	187	1	4
β-strand	190-192	3	5
β-strand	195-201	7	4
α-helix	205-214	10
β-strand	220-224	5	4
α-helix	231-233	3
β-strand	236-241	6	4
β-strand	250-252	3	5
β-strand	256-260	5	4
α-helix	263-268	6
β-strand	278-284	7	6
β-strand	286-293	8	6
α-helix	296-305	10
β-strand	311-315	5	6
α-helix	316	1
α-helix	318-320	3
β-strand	326-332	7	6
β-strand	340-351	12	6
α-helix	353-358	6
α-helix	361-363	3
β-strand	384-389	6	7
β-strand	395-402	8	7
β-strand	407-410	4	7
α-helix	413-415	3
α-helix	421-423	3
β-strand	424-428	5	7
β-strand	432	1	8
β-strand	443-450	8	7
β-strand	464-468	5	7
α-helix	471-474	4
β-strand	475	1	9
β-strand	478	1	9
β-strand	482	1	10
α-helix	483-485	3
α-helix	486-488	3
β-strand	496-500	5	10
β-strand	513	1	8
α-helix	514	1
β-strand	515-518	4	10
β-strand	521-522	2	10
α-helix	524-530	7
β-strand	540-543	4	10
β-strand	560-565	6	10
β-strand	568-575	8	10
α-helix	587	1
β-strand	588-592	5	10
α-helix	593-596	4
α-helix	597-604	8

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	4-8	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Coagulation factor XI	A	protein	607	Homo sapiens	P03951 (AlphaFold model)
Asn-pro-ile-ser-asp-phe-pro-asp	B	protein	8	Homo sapiens	P01042 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5I25_1 Coagulation factor XI (chains A)
ECVTQLLKDTCFEGGDITTVFTPSAKYCQVVCTYHPRCLLFTFTAESPSEDPTRWFTCVL
KDSVTETLPRVNRTAAISGYSFKQCSHQISACNKDIYVDLDMKGINYNSSVAKSAQECQE
RCTDDVHCHFFTYATRQFPSLEHRNICLLKHTQTGTPTRITKLDKVVSGFSLKSCALSNL
ACIRDIFPNTVFADSNIDSVMAPDAFVCGRICTHHPGCLFFTFFSQEWPKESQRNLCLLK
TSESGLPSTRIKKSKALSGFSLQSCRHSIPVFCHSSFYHDTDFLGEELDIVAAKSHEACQ
KLCTNAVRCQFFTYTPAQASCNEGKGKCYLKLSSNGSPTKILHGRGGISGYTLRLCKMDN
ECTTKIKPRIVGGTASVRGEWPWQVTLHTTSPTQRHLCGGSIIGNQWILTAAHCFYGVES
PKILRVYSGILNQSEIKEDTSFFGVQEIIIHDQYKMAESGYDIALLKLETTVNYTDSQRP
ICLPSKGDRNVIYTDCWVTGWGYRKLRDKIQNTLQKAKIPLVTNEECQKRYRGHKITHKM
ICAGYREGGKDACKGDSGGPLSCKHNEVWHLVGITSWGEGCAQRERPGVYTNVVEYVDWI
LEKTQAV

Sequence of entity 2 (B), FASTA

>5I25_2 ASN-PRO-ILE-SER-ASP-PHE-PRO-ASP (chains B)
NPISDFPD

Ligands and cofactors

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

Primary citation

A novel DFP tripeptide motif interacts with the coagulation factor XI apple 2 domain. Wong, S.S., stergaard, S., Hall, G. et al. Blood (2016) 127:2915-2923. DOI 10.1182/blood-2015-10-676122 · 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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