SMTL ID : 3vi4.1 (1 other biounit)

Crystal structure of alpha5beta1 integrin headpiece in complex with RGD peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x ARG- GLY- ASP: RGD peptide(Non-covalent)

ARG-GLY-ASP.1: 15 residues within 4Å: Chain A: Y.186, F.187, Q.189, Q.221, S.224, D.227 Chain B: S.132, Y.133, S.134, G.223, N.224, L.225, S.227, E.229 Ligands: MG.13 12 PLIP interactions: 7 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:S.132, B:Y.133, B:S.134, B:N.224, B:N.224, B:N.224, B:L.225, A:Q.189, A:Q.221, A:Q.221 Hydrophobic interactions: A:F.187 Salt bridges: A:D.227

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.2: 7 residues within 4Å: Chain A: S.241, G.242, D.243, N.266, S.268, D.269, L.273 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.3: 9 residues within 4Å: Chain A: R.220, Q.221, A.222, S.223, Y.226, Y.261, S.272, L.273, N.275 No protein-ligand interaction detected (PLIP)

5 x CA: CALCIUM ION(Non-covalent)

CA.4: 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.5: 6 residues within 4Å: Chain A: D.293, N.295, D.297, L.299, D.301, Q.329 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.6: 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:Y.366, A:D.368 CA.7: 5 residues within 4Å: Chain A: D.424, D.426, N.428, Y.430, D.432 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.424, A:D.426, A:Y.430, A:D.432, A:D.432 CA.12: 6 residues within 4Å: Chain B: E.169, N.224, D.226, S.227, P.228, E.229 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.169, B:D.226, B:D.226, B:P.228, B:E.229

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

NAG.8: 6 residues within 4Å: Chain A: P.15, G.16, K.41, N.43, L.50, Q.51 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.43, A:Q.51 NAG.9: 3 residues within 4Å: Chain A: P.28, N.141, F.142 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.28 NAG.10: 3 residues within 4Å: Chain A: N.256, Y.259, S.277 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.256, A:S.277 NAG.11: 5 residues within 4Å: Chain A: T.502, E.504, N.568, F.569, S.570 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:E.504 Hydrogen bonds: A:E.504 NAG.14: 2 residues within 4Å: Chain B: W.247, N.249 No protein-ligand interaction detected (PLIP) NAG.15: 3 residues within 4Å: Chain B: Y.380, G.384, N.386 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.384

1 x MG: MAGNESIUM ION(Non-covalent)

MG.13: 6 residues within 4Å: Chain B: D.130, S.132, S.134, E.229, D.259 Ligands: ARG-GLY-ASP.1 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:S.132, B:S.134, B:E.229

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nagae, M. et al., Crystal structure of alpha5beta1 integrin ectodomain: Atomic details of the fibronectin receptor. J.Cell Biol. (2012)

Release Date

2012-02-22

Peptides

Integrin alpha-5: A
Integrin beta-1: B
SG/19 Fab fragment (Light chain): C
SG/19 Fab fragment (Heavy chain): D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
E

D
F

Integrin alpha-5

Integrin beta-1

SG/19 Fab fragment (Light chain)

SG/19 Fab fragment (Heavy chain)

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