SMTL ID : 9p95.1

CryoEM structure of integrin alpha4beta7 bound to MAdCAM-1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.05 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.1: 3 residues within 4Å: Chain A: G.62, E.137, N.138 No protein-ligand interaction detected (PLIP)

3 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.2: 7 residues within 4Å: Chain A: D.209, L.210, N.229, T.231, T.232, T.266, I.286 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.231 NAG-NAG-BMA.3: 7 residues within 4Å: Chain A: N.79, S.81, V.82, P.109, N.110, G.111, R.122 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.4: 6 residues within 4Å: Chain A: F.516, Y.517, N.518, A.580, Y.581, H.582 No protein-ligand interaction detected (PLIP)

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

NAG.5: 5 residues within 4Å: Chain A: N.480, T.482, K.483, A.619, R.620 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.619 NAG.12: 3 residues within 4Å: Chain B: W.277, R.278, N.279 No protein-ligand interaction detected (PLIP) NAG.13: 6 residues within 4Å: Chain B: L.220 Chain C: G.40, A.41, S.42, R.82, N.83 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.40

3 x CA: CALCIUM ION(Non-covalent)

CA.6: 6 residues within 4Å: Chain A: D.314, L.315, N.316, D.318, F.320, D.322 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.314, A:D.318, A:F.320, A:D.322, A:D.322 CA.7: 5 residues within 4Å: Chain A: D.377, D.379, D.381, F.383, D.385 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.377, A:D.379, A:D.381, A:F.383, A:D.385 CA.8: 6 residues within 4Å: Chain A: D.439, D.441, N.443, Y.445, D.447, T.463 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.439, A:D.441, A:Y.445, A:D.447, A:D.447

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

MN.9: 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 MN.10: 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.166, B:D.289 MN.11: 6 residues within 4Å: Chain B: S.161, S.163, S.257, E.259, D.290 Chain C: D.64 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:S.161, B:S.163, B:E.259, B:D.290

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-4: A
Integrin beta-7: B
Mucosal addressin cell adhesion molecule 1: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Integrin alpha-4

Integrin beta-7

Mucosal addressin cell adhesion molecule 1

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