3BG8: Factor XIa

Crystal structure of Factor XIa in complex with Clavatadine A. Determined by X-ray diffraction at 1.6 Å resolution. Released 9 Dec 2008.

Method: X-ray diffraction
Resolution: 1.6 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,179
Mol. weight: 27.64 kDa
Ligands: G0R, BEN
Released: 9 Dec 2008

Explore 3BG8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3BG8 contains 12 α-helices and 21 β-strands across 1 chain. 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: 12 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	371	1	1
β-strand	374-375	2	2
α-helix	376-377	2
β-strand	384-389	6	3
β-strand	395-404	10	3
β-strand	407-410	4	3
α-helix	412-415	4
α-helix	421-423	3
β-strand	424-427	4	3
β-strand	432	1	4
α-helix	433-435	3
β-strand	443-450	8	3
α-helix	457-459	3
β-strand	464-468	5	3
β-strand	475	1	5
β-strand	478	1	5
α-helix	480-481	2
β-strand	482	1	2
α-helix	483-485	3
α-helix	486-489	4
β-strand	496-500	5	2
β-strand	513	1	4
α-helix	514	1
β-strand	515-518	4	2
β-strand	521-522	2	2
α-helix	524-530	7
β-strand	540-543	4	2
β-strand	551	1	1
β-strand	560-565	6	2
β-strand	568-577	10	2
β-strand	588-592	5	2
α-helix	593-596	4
α-helix	597-604	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Coagulation factor XIa light chain	A	protein	238	Homo sapiens	P03951 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3BG8_1 Coagulation factor XIa light chain (chains A)
IVGGTASVRGEWPWQVTLHTTSPTQRHLCGGSIIGNQWILTAAHCFYGVESPKILRVYSG
ILNQSEIKEDTSFFGVQEIIIHDQYKMAESGYDIALLKLETTVNYTDSQRPISLPSKGER
NVIYTDCWVTGWGYRKLRDKIQNTLQKAKIPLVTNEECQKRYRGHKITHKMICAGYREGG
KDACKGDSGGPLSCKHNEVWHLVGITSWGEGCAQRERPGVYTNVVEYVDWILEKTQAV

Ligands and cofactors

ID	Name	Formula	Copies
G0R	N-(4-carbamimidamidobutyl)ethanamide	C7 H16 N4 O	1
BEN	Benzamidine	C7 H8 N2	1

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

Primary citation

Clavatadine A, a natural product with selective recognition and irreversible inhibition of factor XIa. Buchanan, M.S., Carroll, A.R., Wessling, D. et al. J Med Chem (2008) 51:3583-3587. DOI 10.1021/jm800314b · 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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