SMTL ID : 9ef2.1

Cryo-EM structure of alpha5beta1 integrin in complex with NeoNectin candidate 2, open conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

3 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 A: G.57, K.82, N.84, Q.92 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain A: N.297, Y.300 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 5 residues within 4Å: Chain A: S.282, N.307, S.309, D.310, L.314 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[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-MAN-MAN.4: 7 residues within 4Å: Chain A: Q.262, A.263, Y.267, Y.302, S.313, L.314, N.316 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.263, A:Y.267 Hydrogen bonds: A:Y.267

1 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.5: 3 residues within 4Å: Chain A: L.98, N.182, F.183 No protein-ligand interaction detected (PLIP)

3 x CA: CALCIUM ION(Non-covalent)

CA.6: 5 residues within 4Å: Chain A: D.334, N.336, D.338, L.340, D.342 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.338, A:D.338, A:L.340, A:D.342, A:D.342 CA.7: 4 residues within 4Å: Chain A: S.282, D.284, T.286, D.288 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:S.282, A:D.284, A:T.286, A:D.288, A:D.288 CA.8: 4 residues within 4Å: Chain A: D.403, D.405, Y.407, D.409 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.403, A:D.403, A:D.405, A:Y.407, A:D.409

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

NAG.9: 2 residues within 4Å: Chain B: N.205, N.212 No protein-ligand interaction detected (PLIP) NAG.10: 1 residues within 4Å: Chain B: N.269 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.269 NAG.11: 1 residues within 4Å: Chain B: N.363 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.363

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

MN.12: 6 residues within 4Å: Chain B: S.152, S.154, S.247, E.249, A.280 Chain C: D.31 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Metal complexes: B:S.152, B:S.154, B:E.249, C:D.31 MN.13: 4 residues within 4Å: Chain B: S.154, D.157, D.158, D.279 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:S.154, B:D.157, B:D.157, B:D.158, B:D.279 MN.14: 6 residues within 4Å: Chain B: E.189, N.244, D.246, S.247, P.248, E.249 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.189, B:D.246, B:D.246, B:P.248, B:E.249

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, X. et al., De Novo Design of Integrin alpha 5 beta 1 Modulating Proteins to Enhance Biomaterial Properties. Adv Mater (2025)

Release Date

2025-06-18

Peptides

Integrin alpha-5: A
Integrin beta-1: B
NeoNectin candidate 2: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Integrin alpha-5

Integrin beta-1

NeoNectin candidate 2

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