SMTL ID : 7ceb.1

Crystal structure of alpha6beta1 integrin headpiece

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.89 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

4 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: D.301, N.303, D.305, W.307, D.309 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.301, A:D.305, A:W.307, A:D.309, H2O.1 CA.2: 5 residues within 4Å: Chain A: D.363, N.365, D.367, Y.369, D.371 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.363, A:D.367, A:Y.369, A:D.371, A:D.371 CA.3: 5 residues within 4Å: Chain A: D.418, D.420, N.422, Y.424, D.426 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.418, A:D.420, A:Y.424, A:D.426, A:D.426 CA.6: 6 residues within 4Å: Chain B: E.169, N.224, D.226, S.227, P.228, E.229 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.169, B:D.226, B:D.226, B:P.228

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

NAG.4: 4 residues within 4Å: Chain A: P.228, V.229, P.230, N.261 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.228 NAG.5: 2 residues within 4Å: Chain A: R.345, N.347 No protein-ligand interaction detected (PLIP) NAG.8: 2 residues within 4Å: Chain B: N.192, R.220 No protein-ligand interaction detected (PLIP) NAG.9: 5 residues within 4Å: Chain B: E.89, N.249, T.431 Chain D: I.32, T.74 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:I.32, D:T.74 Hydrogen bonds: B:N.249 NAG.10: 3 residues within 4Å: Chain B: D.137, A.342, N.343 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.343 NAG.11: 3 residues within 4Å: Chain B: Y.380, G.384, N.386 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.384, B:N.386

1 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 6 residues within 4Å: Chain B: D.130, S.132, S.134, E.229, D.259, A.260 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.130, B:S.132, B:S.134, B:E.229, B:D.259

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Arimori, T. et al., Structural mechanism of laminin recognition by integrin. Nat Commun (2021)

Release Date

2021-06-23

Peptides

Integrin alpha-6: A
Integrin beta-1: B
TS2/16 VH(S112C)-SARAH: C
TS2/16 VL-SARAH(S37C): D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Integrin alpha-6

Integrin beta-1

TS2/16 VH(S112C)-SARAH

TS2/16 VL-SARAH(S37C)

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