SMTL ID : 9ckv.1

Cryo-EM structure of alpha5beta1 integrin in complex with NeoNectin

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

1 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: 8 residues within 4Å: Chain A: P.56, G.57, S.58, K.82, A.83, N.84, L.91, Q.92 No protein-ligand interaction detected (PLIP)

4 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 6 residues within 4Å: Chain A: N.297, L.298, Y.300, Y.302, N.316, S.318 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 6 residues within 4Å: Chain A: S.282, N.307, S.309, D.310, R.312, L.314 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 6 residues within 4Å: Chain A: Y.67, P.69, L.98, T.109, N.182, F.183 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain B: N.363, S.365 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: 14 residues within 4Å: Chain A: R.261, Q.262, A.263, S.264, Y.267, L.272, Y.302, T.304, S.313, L.314, Y.315, N.316 Chain C: D.54, R.85 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.263

4 x CA: CALCIUM ION(Non-covalent)

CA.7: 6 residues within 4Å: Chain A: D.334, 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.8: 4 residues within 4Å: Chain A: S.282, T.286, D.288, G.308 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:S.282, A:T.286, A:D.288 CA.9: 6 residues within 4Å: Chain A: D.401, D.403, D.405, Y.407, D.409, G.430 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 CA.10: 7 residues within 4Å: Chain A: D.465, D.467, N.469, Y.471, P.472, D.473, G.489 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.467, A:D.467, A:Y.471, A:D.473

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

NAG.11: 6 residues within 4Å: Chain B: S.379, N.403, N.417, I.418, S.419, D.422 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.422 NAG.12: 3 residues within 4Å: Chain B: Y.400, G.404, N.406 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.406

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

MN.13: 7 residues within 4Å: Chain B: D.150, 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.14: 5 residues within 4Å: Chain B: S.154, D.157, D.158, D.279 Chain C: P.33 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.15: 6 residues within 4Å: Chain B: E.189, N.244, D.246, P.248, E.249, H.283 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 for Regenerative Medicine. Biorxiv (2024)

Release Date

2024-07-17

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Integrin alpha-5

Integrin beta-1

NeoNectin