9D3Y: Mannan-binding lectin serine protease 2 B chain

Crystal structure of the catalytic region of human MASP-2 with specific inhibitor Compound S2. Determined by X-ray diffraction at 2.08 Å resolution. Released 16 Apr 2025.

Method: X-ray diffraction
Resolution: 2.08 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,565
Mol. weight: 36.36 kDa
Ligands: A1A1Y
Released: 16 Apr 2025

Explore 9D3Y in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9D3Y contains 13 α-helices and 26 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, 26 β-strands

Element	Residues	Length	Sheet
α-helix	369-372	4
β-strand	375-379	5	1
β-strand	391-396	6	1
β-strand	401-404	4	2
β-strand	409-412	4	1
β-strand	418-420	3	1
β-strand	429-432	4	2
α-helix	433	1
β-strand	446	1	3
β-strand	449-450	2	4
α-helix	451-452	2
β-strand	459-463	5	5
β-strand	467-473	7	5
β-strand	477-480	4	5
α-helix	482-490	9
β-strand	496-499	4	5
β-strand	503	1	6
β-strand	510-519	10	5
β-strand	534-538	5	5
α-helix	541-544	4
α-helix	550-551	2
β-strand	552	1	4
α-helix	553-555	3
α-helix	558-561	4
β-strand	567-572	6	4
β-strand	575	1	7
β-strand	581	1	7
β-strand	584	1	6
β-strand	586-592	7	4
α-helix	593-594	2
α-helix	595-601	7
α-helix	608	1
β-strand	616-619	4	4
β-strand	627	1	3
β-strand	636-641	6	4
β-strand	646-655	10	4
β-strand	667-671	5	4
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

>9D3Y_1 Mannan-binding lectin serine protease 2 B chain (chains A)
IVDCGPPDDLPSGRVEYITGPGVTTYKAVIQYSCEETFYTMKVNDGKYVCEADGFWTSSK
GEKSLPVCEPVCGLSARTTGGRIYGGQKAKPGDFPWQVLILGGTTAAGALLYDNWVLTAA
HAVYEQKHDASALDIRMGTLKRLSPHYTQAWSEAVFIHEGYTHDAGFDNDIALIKLNNKV
VINSNITPICLPRKEAESFMRTDDIGTASGWGLTQRGFLARNLMYVDIPIVDHQKCTAAY
EKPPYPRGSVTANMLCAGLESGGKDSCRGDSGGALVFLDSETERWFVGGIVSWGSMNCGE
AGQYGVYTKVINYIPWIENIISDF

Ligands and cofactors

ID	Name	Formula	Copies
A1A1Y	(2S)-N-[2-(2-amino-1H-1,3-benzimidazol-5-yl)ethyl]-1-[(2R,4S)-4-phenylpiperidin…	C25 H30 N6 O2	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…
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
9D4D 2.36 Å, Crystal structure of the catalytic region of human MASP-2 with specific inhibitor…
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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