SMTL ID : 4o02.1

AlphaVBeta3 integrin in complex with monoclonal antibody FAB fragment.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.61 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x NAG- NAG- BMA- MAN- BMA- MAN: beta-D-mannopyranose-(1-4)-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-BMA-MAN.1: 5 residues within 4Å: Chain A: E.15, G.16, K.42, N.44, E.52 No protein-ligand interaction detected (PLIP)

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.2: 3 residues within 4Å: Chain A: N.232, D.257, N.260 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: 8 residues within 4Å: Chain A: A.213, Q.214, F.217, M.252, Y.254, S.263, L.264, N.266 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.214, A:Q.214 Hydrophobic interactions: A:A.213, A:F.217

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.4: 4 residues within 4Å: Chain A: E.560, A.584, N.585 Chain B: D.512 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain A: R.248, M.272 Chain B: N.316, N.320 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 6 residues within 4Å: Chain B: S.369, N.371, S.398, I.399, E.400 Ligands: NAG.15 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-3)-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(Post Translational Modification)

NAG-NAG-BMA-MAN-MAN-MAN.5: 3 residues within 4Å: Chain A: T.942, N.943, S.944 No protein-ligand interaction detected (PLIP)

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

NAG.8: 4 residues within 4Å: Chain A: N.492, N.524, T.526, T.567 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.492, A:T.526 NAG.15: 3 residues within 4Å: Chain B: N.99, F.100 Ligands: NAG-NAG.7 No protein-ligand interaction detected (PLIP) NAG.16: 4 residues within 4Å: Chain B: R.530, Y.531, Y.557, N.559 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.530

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

MN.9: 5 residues within 4Å: Chain A: D.230, N.232, D.234, I.236, D.238 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.230, A:N.232, A:D.234, A:D.238, A:D.238 MN.10: 5 residues within 4Å: Chain A: D.284, N.286, D.288, Y.290, D.292 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 MN.11: 5 residues within 4Å: Chain A: D.349, D.351, D.353, F.355, D.357 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.349, A:D.351, A:D.353, A:F.355, A:D.357 MN.12: 5 residues within 4Å: Chain A: D.413, D.415, N.417, Y.419, D.421 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.413, A:D.415, A:Y.419, A:D.421, A:D.421 MN.17: 5 residues within 4Å: Chain B: S.123, M.124, D.126, D.127, M.335 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:S.123, B:D.126, B:D.126, B:D.127, B:M.335

2 x NO3: NITRATE ION(Non-functional Binders)

NO3.13: 7 residues within 4Å: Chain A: K.194, S.201, I.202, K.203 Chain C: H.55 Chain D: L.100, Y.107 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain A Hydrogen bonds: D:Y.107, D:Y.107, A:S.201, A:K.203, A:K.203 NO3.14: 9 residues within 4Å: Chain A: P.141, R.143, S.201, I.202, Y.204, Q.207 Chain D: T.28, S.31, F.32 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:R.143, A:Q.207, A:Q.207, D:T.28, D:S.31

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mahalingam, B. et al., Atomic basis for the species-specific inhibition of alpha V integrins by monoclonal antibody 17E6 is revealed by the crystal structure of alpha V beta 3 ectodomain-17E6 Fab complex. J.Biol.Chem. (2014)

Release Date

2014-04-02

Peptides

Integrin alpha-V: A
Integrin beta-3: B
17E6 light chain: C
17E6 heavy chain: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
L

D
H

Integrin alpha-V

Integrin beta-3

17E6 light chain

17E6 heavy chain

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