5L73: MAM domain of human neuropilin-1

MAM domain of human neuropilin-1. Determined by X-ray diffraction at 2.24 Å resolution. Released 26 Oct 2016.

Method: X-ray diffraction
Resolution: 2.24 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,981
Mol. weight: 44.74 kDa
Ligands: CA, BCN, TAM
Released: 26 Oct 2016

Explore 5L73 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5L73 contains 8 α-helices and 33 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: 4 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	643-646	4
β-strand	650	1	1
β-strand	653-654	2	2
β-strand	657-658	2	2
β-strand	664-665	2	3
β-strand	671	1	3
β-strand	674-677	4	4
β-strand	685	1	5
β-strand	690	1	5
β-strand	691-696	6	4
α-helix	699-701	3
β-strand	705-713	9	3
β-strand	720-728	9	4
β-strand	734-742	9	3
α-helix	743	1
β-strand	749-756	8	3
β-strand	763	1	6
β-strand	764-770	7	4
β-strand	777-785	9	3
α-helix	786	1
β-strand	792-800	9	4

Chain B: 4 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	650	1	7
β-strand	653-654	2	8
β-strand	657-658	2	8
β-strand	664-665	2	9
β-strand	671	1	9
α-helix	673	1
β-strand	674-677	4	10
β-strand	691-696	6	10
α-helix	699-701	3
β-strand	705-709	5	9
α-helix	710-713	4
β-strand	720-728	9	10
β-strand	734-742	9	9
β-strand	748-756	9	9
β-strand	764-770	7	10
β-strand	777-785	9	9
β-strand	792-799	8	10
β-strand	804	1	6
α-helix	806-809	4
β-strand	811	1	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Neuropilin-1	A, B	protein	192	Homo sapiens	O14786 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5L73_1 Neuropilin-1 (chains A, B)
ADEKPDVIDDDIQDEFPDYGFNCEFGWGSHKTFCHWEHDNHVQLKWSVLTSKTGPIQDHT
GDGNFIYSQADENQKGKVARLVSPVVYSQNSAHCMTFWYHMSGSHVGTLRVKLRYQKPEE
YDQLVWMAIGHQGDHWKEGRVLLHKSLKLYQVIFEGEIGKGNLGGIAVDDISINNHISQE
DCAKPAHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	4
BCN	Bicine	C6 H13 N O4	2
TAM	Tris(hydroxyethyl)aminomethane	C7 H17 N O3	1

Primary citation

Crystal Structure of the Neuropilin-1 MAM Domain: Completing the Neuropilin-1 Ectodomain Picture. Yelland, T., Djordjevic, S. Structure (2016) 24:2008-2015. DOI 10.1016/j.str.2016.08.017 · PubMed

Other PDB entries of the same protein (UniProt O14786 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6FMC 0.9 Å, Neuropilin1-b1 domain in complex with EG01377, 0.9 Angstrom structure
6TKK 1.06 Å, Neuropilin 1-b1 domain in a complex with the C-terminal VEGFB186 peptide
8PFE 1.35 Å, Crystal Structure of an Hexavariant of the b1 Domain of Human Neuropilin-1 in Complex…
5JGI 1.38 Å, X-ray structure of neuropilin-1 b1 domain complexed with M45 compound
5C7G 1.45 Å, Crystal Structure of the b1 Domain of Human Neuropilin-1 in complex with a bicine molecule
5IJR 1.52 Å, X-ray structure of neuropilin-1 b1 domain complexed with Arg-1 ligand.
9EOU 1.55 Å, Crystal Structure of the b1b2 domains from Human Neuropilin-1 in complex with a peptide.
7O1N 1.56 Å, Crystal Structure of Human Neuropilin-1 b1 Domain mutant - Y297A
9S57 1.57 Å, The b1 and b2 domains of neuropilin-1 with a bound VGF TLQP-21 peptide
9F6B 1.57 Å, Human neuropilin-1 in a complex with a quinoline based antagonists
5IYY 1.6 Å, X-ray structure of neuropilin-1 b1 domain complexed with Arg-4 ligand.
5JGQ 1.6 Å, X-ray structure of neuropilin-1 b1 domain complexed with Arg-7 ligand.

Browse structure collections

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