SMTL ID : 7nxd.1

Cryo-EM structure of human integrin alpha5beta1 in the half-bent conformation

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

5 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: P.15, N.43, L.50 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.3: 2 residues within 4Å: Chain A: N.256, Y.259 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.11: 3 residues within 4Å: Chain B: K.378, Y.380, N.386 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.13: 4 residues within 4Å: Chain B: H.458, E.459, N.461, R.475 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.14: 3 residues within 4Å: Chain B: N.30, T.32, D.59 No protein-ligand interaction detected (PLIP)

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.2: 3 residues within 4Å: Chain A: R.27, Q.66, N.141 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.4: 4 residues within 4Å: Chain A: D.243, N.266, S.268, D.269 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain A: E.504, N.568, R.593 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain A: N.489, R.540, E.541 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 2 residues within 4Å: Chain B: E.190, N.192 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain B: W.247, N.249, T.431 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 2 residues within 4Å: Chain B: N.141, N.343 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 2 residues within 4Å: Chain B: N.383, N.397 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.383

1 x NAG- NAG- BMA- MAN- NAG- MAN: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-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-NAG-MAN.5: 7 residues within 4Å: Chain A: R.220, Q.221, Y.226, Y.261, T.263, S.272, N.275 No protein-ligand interaction detected (PLIP)

7 x CA: CALCIUM ION(Non-covalent)

CA.15: 5 residues within 4Å: Chain A: E.239, S.241, D.243, T.245, D.247 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.239, A:S.241, A:D.243, A:T.245, A:D.247 CA.16: 5 residues within 4Å: Chain A: D.293, N.295, D.297, L.299, D.301 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.293, A:D.297, A:L.299, A:D.301, A:D.301 CA.17: 5 residues within 4Å: Chain A: D.360, D.362, D.364, Y.366, D.368 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.360, A:D.362, A:D.364, A:D.364, A:Y.366 CA.18: 5 residues within 4Å: Chain A: D.424, D.426, N.428, Y.430, D.432 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.424, A:D.426, A:Y.430, A:D.432 CA.19: 6 residues within 4Å: Chain A: C.604, G.605, E.606, D.607, I.609, E.644 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.607, A:I.609, A:E.644, A:E.644 CA.22: 5 residues within 4Å: Chain B: S.134, M.135, D.137, D.138, A.342 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:S.134, B:D.137, B:A.342 CA.23: 6 residues within 4Å: Chain B: E.169, N.224, D.226, P.228, E.229, H.263 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.226, B:D.226, B:P.228, B:E.229

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

NAG.20: 5 residues within 4Å: Chain A: F.461, S.471, C.481, N.483, E.545 No protein-ligand interaction detected (PLIP)

1 x MG: MAGNESIUM ION(Non-covalent)

MG.21: 2 residues within 4Å: Chain B: S.132, E.229 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:S.132, B:E.229

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schumacher, S. et al., Structural insights into integrin alpha 5 beta 1 opening by fibronectin ligand. Sci Adv (2021)

Release Date

2021-08-25

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Integrin alpha-5

Integrin beta-1

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