SMTL ID : 9p98.1

CryoEM structure of the open integrin alphaEbeta7 bound to fab LF61

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.93 Å

Oligo State

hetero-1-1-1-1-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: 12 residues within 4Å: Chain A: A.396, H.398, Y.399, 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: 8 residues within 4Å: Chain A: N.726, T.728, L.749, G.750, L.752, Q.790, Q.792 Chain D: K.36 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, T.324, N.327 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.324, A:T.324, A:N.327 NAG.5: 3 residues within 4Å: Chain A: N.271, I.272, T.273 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.273 Hydrogen bonds: A:N.271 NAG.12: 3 residues within 4Å: Chain B: W.277, R.278, N.279 No protein-ligand interaction detected (PLIP)

6 x CA: CALCIUM ION(Non-covalent)

CA.6: 7 residues within 4Å: Chain A: D.654, I.655, S.656, G.657, D.658, L.660, D.662 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.654, A:S.656, A:D.658, A:L.660, A:D.662 CA.7: 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:S.528, A:D.530 CA.8: 8 residues within 4Å: Chain A: D.586, L.587, S.588, D.590, L.592, D.594, N.619, G.620 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.586, A:S.588, A:L.592, A:D.594, A:D.594 CA.9: 6 residues within 4Å: Chain A: E.390 Chain B: S.161, S.163, E.259, D.289, D.290 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Metal complexes: B:S.161, B:S.163, B:E.259, A:E.390 CA.10: 7 residues within 4Å: Chain B: D.198, F.204, 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 CA.11: 4 residues within 4Å: Chain B: S.163, D.166, D.167, D.289 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:S.163, B:D.166, B:D.167

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
Fab LF61 Heavy Chain: C
Fab LF61 Light Chain: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
H

D
L

Integrin alpha-E

Integrin beta-7

Fab LF61 Heavy Chain

Fab LF61 Light Chain

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