SMTL ID : 9dia.1

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

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: 7 residues within 4Å: Chain A: S.282, N.307, G.308, S.309, D.310, R.312, L.314 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 7 residues within 4Å: Chain A: G.57, S.58, K.82, A.83, N.84, L.91, Q.92 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain B: D.157, A.362, N.363 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- NAG: alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]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-NAG.2: 9 residues within 4Å: Chain A: R.261, Q.262, A.263, S.264, Y.267, Y.302, S.313, L.314, N.316 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.262

1 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.3: 3 residues within 4Å: Chain A: R.68, N.182, F.183 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.182

3 x CA: CALCIUM ION(Non-covalent)

CA.6: 7 residues within 4Å: Chain A: D.465, D.467, N.469, Y.471, D.473, R.488, G.489 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.465, A:D.467, A:Y.471, A:D.473 CA.8: 7 residues within 4Å: Chain A: D.334, V.335, N.336, D.338, L.340, D.342, Q.370 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.334, A:D.338, A:L.340, A:D.342, A:D.342 CA.9: 6 residues within 4Å: Chain A: D.401, D.403, D.405, Y.407, D.409, G.430 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.405, A:Y.407, A:D.409, A:D.409

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

NAG.7: 4 residues within 4Å: Chain A: N.297, Y.300, S.318, G.319 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.297 NAG.10: 2 residues within 4Å: Chain B: N.269, T.451 No protein-ligand interaction detected (PLIP) NAG.11: 3 residues within 4Å: Chain B: Y.400, G.404, N.406 No protein-ligand interaction detected (PLIP) NAG.12: 2 residues within 4Å: Chain B: N.403, N.417 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.403, B:N.417 NAG.13: 2 residues within 4Å: Chain B: N.212, R.240 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.212

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

MN.14: 5 residues within 4Å: Chain B: D.150, S.152, S.154, E.249 Chain C: D.31 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain B Metal complexes: C:D.31, B:S.152, B:S.154, B:E.249 MN.15: 6 residues within 4Å: Chain B: E.189, N.244, D.246, P.248, E.249, H.283 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.189, B:D.246, B:D.246, B:P.248

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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