SMTL ID : 6om1.1 (3 other biounits)

Crystal structure of an atypical integrin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.66 Å

Oligo State

hetero-1-1-mer

Ligands

3 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.1: 8 residues within 4Å: Chain A: E.449, Y.451, P.452, N.459, T.461, C.473, F.474, N.475 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.449 NAG-NAG-BMA-MAN.3: 3 residues within 4Å: Chain A: D.257, N.260, S.262 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.7: 7 residues within 4Å: Chain B: Q.75, L.100, Y.103, K.232, E.233, N.414, E.415 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.100 Hydrogen bonds: B:Q.75

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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.2: 8 residues within 4Å: Chain A: E.15, G.16, S.17, K.42, A.43, N.44, V.51, E.52 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: 9 residues within 4Å: Chain A: A.213, Q.214, F.217, M.252, Y.254, S.263, L.264, Y.265, N.266 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.214, A:Q.214 Hydrophobic interactions: A:A.213, A:F.217

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

NAG-NAG.5: 4 residues within 4Å: Chain B: N.191, T.193, E.194, K.197 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:K.197 NAG-NAG.6: 2 residues within 4Å: Chain B: R.378, N.379 No protein-ligand interaction detected (PLIP)

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

NAG.8: 5 residues within 4Å: Chain A: K.502, F.559, E.561, P.584, N.586 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.559 Hydrogen bonds: A:N.586 NAG.16: 3 residues within 4Å: Chain A: S.305 Chain B: Y.358, N.360 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.358 Hydrogen bonds: B:N.360

5 x CA: CALCIUM ION(Non-covalent)

CA.9: 7 residues within 4Å: Chain A: D.230, F.231, N.232, D.234, I.236, D.238, G.258 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.230, A:D.234, A:D.234, A:I.236, A:D.238 CA.10: 8 residues within 4Å: Chain A: D.284, I.285, N.286, D.288, Y.290, D.292, L.319, Q.320 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.284, A:D.288, A:Y.290, A:D.292, A:D.292 CA.11: 8 residues within 4Å: Chain A: D.349, L.350, D.351, D.353, F.355, N.356, D.357, N.377 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.351, A:D.353, A:F.355, A:D.357, H2O.1 CA.12: 7 residues within 4Å: Chain A: D.414, I.415, D.416, N.418, Y.420, D.422, A.438 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.414, A:D.416, A:Y.420, A:D.422, H2O.1 CA.15: 6 residues within 4Å: Chain B: D.151, N.207, D.209, P.211, E.212, H.247 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.151, B:D.209, B:D.209, B:P.211, B:E.212

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.13: 2 residues within 4Å: Chain A: Q.394, W.395 No protein-ligand interaction detected (PLIP) EDO.17: 1 residues within 4Å: Chain B: N.129 No protein-ligand interaction detected (PLIP) EDO.18: 9 residues within 4Å: Chain A: F.21, W.93, A.96, P.110, L.111, F.159 Chain B: K.253, L.254, G.256 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:F.159, B:L.254, B:G.256

1 x MG: MAGNESIUM ION(Non-covalent)

MG.14: 5 residues within 4Å: Chain B: D.112, S.114, S.116, E.212 Ligands: MES.19 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.114, B:E.212, H2O.6, H2O.6

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.19: 10 residues within 4Å: Chain A: Y.178 Chain B: S.114, A.115, S.116, G.206, N.207, I.208, T.210, E.212 Ligands: MG.14 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.114, B:A.115, B:N.207, B:N.207

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, J. et al., General structural features that regulate integrin affinity revealed by atypical alpha V beta 8. Nat Commun (2019)

Release Date

2019-12-11

Peptides

Integrin alpha-V: A
Integrin beta-8: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Integrin alpha-V

Integrin beta-8

Related Entries With Identical Sequence