SMTL ID : 7cec.1

Structure of alpha6beta1 integrin in complex with laminin-511

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-1-1-mer

Ligands

1 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: 4 residues within 4Å: Chain C: R.426, L.427, H.477, N.634 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.427

4 x CA: CALCIUM ION(Non-covalent)

CA.2: 6 residues within 4Å: Chain A: D.301, N.303, D.305, W.307, D.309, N.333 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.305, A:D.305, A:W.307, A:D.309, A:D.309 CA.3: 6 residues within 4Å: Chain A: D.363, N.365, D.367, Y.369, D.371, H.388 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.4: 6 residues within 4Å: Chain A: D.418, D.420, N.422, Y.424, D.426, S.441 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.418, A:D.420, A:D.426, A:D.426, A:S.441 CA.13: 6 residues within 4Å: Chain C: D.140, L.157, E.211, L.213, N.215, D.566 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.140, C:L.157, C:E.211, C:L.213, C:D.566

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

NAG.5: 3 residues within 4Å: Chain A: A.260, N.261, D.285 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.260 Hydrogen bonds: A:N.261, A:D.285 NAG.6: 4 residues within 4Å: Chain A: R.345, L.346, N.347, T.396 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.347 NAG.10: 2 residues within 4Å: Chain B: N.249 Chain G: I.32 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:I.32 NAG.11: 2 residues within 4Å: Chain B: N.343, S.345 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.345, B:S.345 NAG.12: 2 residues within 4Å: Chain B: G.384, N.386 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.384, B:N.386 NAG.14: 6 residues within 4Å: Chain C: F.479, G.595, L.596, P.597, S.599, N.604 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:F.479 Hydrogen bonds: C:L.596, C:P.597, C:S.599

3 x MN: MANGANESE (II) ION(Non-covalent)

MN.7: 6 residues within 4Å: Chain B: E.169, N.224, D.226, P.228, E.229, H.263 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.169, B:E.169, B:D.226, B:D.226, B:P.228 MN.8: 6 residues within 4Å: Chain B: D.130, S.132, S.134, E.229, A.260 Chain E: E.81 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain E Metal complexes: B:S.132, B:S.134, B:E.229, E:E.81, E:E.81 MN.9: 4 residues within 4Å: Chain B: S.134, D.137, D.138, D.259 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:S.134, B:D.137, B:D.137, B:D.138, 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
Laminin subunit alpha-5: C
Laminin subunit beta-1: D
Laminin subunit gamma-1: E
TS2/16 VH(S112C)-SARAH,TS2/16 VH(S112C)-SARAH: F
TS2/16 VL-SARAH(S37C),TS2/16 VL-SARAH(S37C): G
HUTS-4 VH(S112C)-SARAH,HUTS-4 VH(S112C)-SARAH: H
HUTS-4 VL(C87Y)-SARAH(S37C),HUTS-4 VL(C87Y)-SARAH(S37C): I

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

Integrin alpha-6

Integrin beta-1

Laminin subunit alpha-5

Laminin subunit beta-1

Laminin subunit gamma-1

TS2/16 VH(S112C)-SARAH,TS2/16 VH(S112C)-SARAH

TS2/16 VL-SARAH(S37C),TS2/16 VL-SARAH(S37C)

HUTS-4 VH(S112C)-SARAH,HUTS-4 VH(S112C)-SARAH

HUTS-4 VL(C87Y)-SARAH(S37C),HUTS-4 VL(C87Y)-SARAH(S37C)

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