SMTL ID : 9p99.1

CryoEM structure of integrin alphaEbeta7 bound to E-cadherin

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.37 Å

Oligo State

hetero-1-1-1-mer

Ligands

2 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 3 residues within 4Å: Chain A: S.47, T.48, N.49 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.2: 11 residues within 4Å: Chain A: A.396, H.398, F.424, S.427, F.442, N.444, Q.445, T.446, A.447, A.453, A.456 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.398, A:H.398

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.3: 5 residues within 4Å: Chain A: N.726, T.728, L.752, Q.790, Q.792 No protein-ligand interaction detected (PLIP)

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

NAG.4: 4 residues within 4Å: Chain A: N.321, T.323 Chain C: N.200, A.201 No protein-ligand interaction detected (PLIP) NAG.5: 4 residues within 4Å: Chain A: R.268, N.271, I.272, T.273 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.268, A:R.268, A:N.271 NAG.10: 5 residues within 4Å: Chain B: Q.272, E.273, W.277, N.279, R.282 No protein-ligand interaction detected (PLIP)

3 x CA: CALCIUM ION(Non-covalent)

CA.6: 5 residues within 4Å: Chain A: D.522, D.524, D.526, S.528, D.530 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.522, A:D.524, A:D.526, A:D.526, A:D.530 CA.7: 7 residues within 4Å: Chain A: D.586, S.588, D.590, L.592, D.594, N.619, G.620 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:S.588, A:D.590, A:D.594 CA.8: 7 residues within 4Å: Chain A: D.654, S.656, D.658, L.660, A.661, D.662, S.676 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:S.656, A:D.658, A:L.660, A:D.662

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

MN.9: 6 residues within 4Å: Chain A: S.210, G.211, S.212, T.279, D.312 Chain C: E.145 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Metal complexes: A:S.210, A:S.212, A:T.279, C:E.145 MN.11: 6 residues within 4Å: Chain A: E.390 Chain B: S.161, S.163, S.257, E.259, D.290 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Metal complexes: A:E.390, B:S.161, B:S.163, B:E.259, B:D.290 MN.12: 5 residues within 4Å: Chain B: S.163, M.164, D.166, D.167, D.289 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:S.163, B:D.166, B:D.167, B:D.289 MN.13: 6 residues within 4Å: Chain B: D.198, N.254, D.256, P.258, E.259, H.293 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.198, B:D.256, B:D.256, B:P.258

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hollis, J.A. et al., Molecular exaptation by the integrin alpha I domain. Sci Adv (2025)

Release Date

2025-09-24

Peptides

Integrin alpha-E: A
Integrin beta-7: B
Cadherin-1: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Integrin alpha-E

Integrin beta-7

Cadherin-1

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