SMTL ID : 7p2d.1

Structure of alphaMbeta2/Cd11bCD18 headpiece in complex with a nanobody

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

hetero-1-1-1-mer

Ligands

4 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 9 residues within 4Å: Chain A: T.322, Y.356, F.373, N.375, M.376, T.377, R.378, V.379, M.383 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.322 NAG-NAG.2: 5 residues within 4Å: Chain A: I.38, A.41, N.42, Q.43, N.70 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 6 residues within 4Å: Chain A: T.660, D.662, R.685, N.719, F.720, S.721 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain B: A.92, F.93, N.94, Q.390 No protein-ligand interaction detected (PLIP)

2 x CA: CALCIUM ION(Non-covalent)

CA.5: 6 residues within 4Å: Chain A: D.514, V.515, N.516, D.518, L.520, D.522 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.514, A:D.518, A:L.520, A:D.522, A:D.522 CA.6: 5 residues within 4Å: Chain A: D.577, T.579, D.581, L.583, D.585 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:T.579, A:D.581, A:D.581, A:L.583, A:D.585

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.7: 3 residues within 4Å: Chain B: S.141, R.143, N.190 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.143

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jensen, R.K. et al., Structural insights into the function-modulating effects of nanobody binding to the integrin receptor alpha M beta 2. J.Biol.Chem. (2022)

Release Date

2022-05-04

Peptides

Isoform 2 of Integrin alpha-M: A
Integrin beta: B
hCD11bNb1 nanobody: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Isoform 2 of Integrin alpha-M

Integrin beta

hCD11bNb1 nanobody

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