9D4D: Mannan-binding lectin serine protease 2 B chain

Crystal structure of the catalytic region of human MASP-2 with specific inhibitor Compound S3. Determined by X-ray diffraction at 2.36 Å resolution. Released 16 Apr 2025.

Method: X-ray diffraction
Resolution: 2.36 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,575
Mol. weight: 36.37 kDa
Ligands: A1A10
Released: 16 Apr 2025

Explore 9D4D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9D4D contains 13 α-helices and 28 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: 13 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	365	1	1
α-helix	369-372	4
β-strand	375-379	5	2
β-strand	387	1	1
β-strand	391-396	6	2
β-strand	401-404	4	3
β-strand	409-412	4	2
β-strand	418-420	3	2
α-helix	427-428	2
β-strand	429-432	4	3
α-helix	433	1
β-strand	446	1	4
β-strand	449-450	2	5
α-helix	451-452	2
β-strand	459-463	5	6
β-strand	468-473	6	6
β-strand	477-480	4	6
α-helix	482-489	8
β-strand	496-499	4	6
β-strand	503	1	7
β-strand	510-519	10	6
β-strand	534-538	5	6
α-helix	541-544	4
α-helix	550-551	2
β-strand	552	1	5
α-helix	553-554	2
α-helix	556-561	6
β-strand	567-572	6	5
β-strand	575	1	8
β-strand	581	1	8
β-strand	584	1	7
β-strand	586-592	7	5
α-helix	595-601	7
α-helix	608	1
β-strand	616-619	4	5
β-strand	627	1	4
β-strand	636-641	6	5
β-strand	646-655	10	5
β-strand	667-671	5	5
α-helix	672-675	4
α-helix	676-685	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Mannan-binding lectin serine protease 2 B chain	A	protein	324	Homo sapiens	O00187 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9D4D_1 Mannan-binding lectin serine protease 2 B chain (chains A)
IVDCGPPDDLPSGRVEYITGPGVTTYKAVIQYSCEETFYTMKVNDGKYVCEADGFWTSSK
GEKSLPVCEPVCGLSARTTGGRIYGGQKAKPGDFPWQVLILGGTTAAGALLYDNWVLTAA
HAVYEQKHDASALDIRMGTLKRLSPHYTQAWSEAVFIHEGYTHDAGFDNDIALIKLNNKV
VINSNITPICLPRKEAESFMRTDDIGTASGWGLTQRGFLARNLMYVDIPIVDHQKCTAAY
EKPPYPRGSVTANMLCAGLESGGKDSCRGDSGGALVFLDSETERWFVGGIVSWGSMNCGE
AGQYGVYTKVINYIPWIENIISDF

Ligands and cofactors

ID	Name	Formula	Copies
A1A10	2-(2-amino-1H-1,3-benzimidazol-4-yl)-N-{4-[(pyridin-4-yl)methyl]phenyl}acetamide	C21 H19 N5 O	1

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

Primary citation

Small molecule inhibitors of mannan-binding lectin-associated serine Proteases-2 and-3. Nakhla, M.C., Comita, J., Shapiro, A.B. et al. Eur J Med Chem (2025) 289:117238-117238. DOI 10.1016/j.ejmech.2025.117238 · PubMed

Other PDB entries of the same protein (UniProt O00187 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3TVJ 1.28 Å, Catalytic fragment of MASP-2 in complex with its specific inhibitor developed by…
9D40 1.76 Å, Crystal structure of the catalytic region of human MASP-2 with specific inhibitor Analog…
9D17 1.97 Å, Crystal structure of the catalytic region of human MASP-2 with specific inhibitor…
9D3Y 2.08 Å, Crystal structure of the catalytic region of human MASP-2 with specific inhibitor…
1ZJK 2.18 Å, Crystal structure of the zymogen catalytic region of human MASP-2
1Q3X 2.23 Å, Crystal structure of the catalytic region of human MASP-2
7PQN 2.4 Å, Catalytic fragment of MASP-2 in complex with ecotin
1SZB 2.5 Å, Crystal structure of the human MBL-associated protein 19 (MAp19)
5JPM 3.75 Å, Structure of the complex of human complement C4 with MASP-2 rebuilt using iMDFF

Browse structure collections

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