SMTL ID : 9b9k.1

Integrin alpha-5 beta-1 in complex with MINT1526A Fab

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.70 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

4 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: 7 residues within 4Å: Chain A: G.57, S.58, K.82, A.83, N.84, L.91, Q.92 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.3: 3 residues within 4Å: Chain B: N.161, N.363, S.365 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.6: 7 residues within 4Å: Chain A: S.282, D.284, N.307, G.308, S.309, D.310, L.314 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.10: 3 residues within 4Å: Chain B: Y.400, G.404, N.406 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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-MAN.2: 16 residues within 4Å: Chain A: R.261, Q.262, A.263, S.264, Y.267, Y.302, T.304, S.313, L.314, Y.315, N.316 Chain D: D.54, G.55, S.70, S.71, S.72 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.267

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.4: 6 residues within 4Å: Chain A: R.68, L.98, P.100, T.109, N.182, F.183 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.98, A:P.100

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.5: 5 residues within 4Å: Chain A: N.297, Y.300, Y.302, S.318, G.319 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 6 residues within 4Å: Chain A: T.543, V.544, E.545, N.609, F.610, S.611 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 2 residues within 4Å: Chain B: N.212, R.240 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain B: R.268, N.269, T.451 No protein-ligand interaction detected (PLIP)

7 x CA: CALCIUM ION(Non-covalent)

CA.11: 9 residues within 4Å: Chain A: E.280, F.281, S.282, G.283, D.284, T.286, E.287, D.288, G.308 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.280, A:D.284, A:T.286, A:D.288, A:D.288 CA.12: 9 residues within 4Å: Chain A: D.334, V.335, N.336, G.337, D.338, L.340, D.342, L.369, 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.13: 7 residues within 4Å: Chain A: D.401, L.402, D.403, D.405, Y.407, D.409, G.430 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.401, A:D.403, A:D.405, A:Y.407, A:D.409 CA.14: 8 residues within 4Å: Chain A: D.465, L.466, D.467, G.468, N.469, Y.471, D.473, G.489 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.465, A:D.467, A:Y.471, A:D.473, A:D.473 CA.15: 6 residues within 4Å: Chain B: S.154, M.155, D.157, D.158, A.362, N.363 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:S.154, B:D.157, B:D.158, B:A.362 CA.16: 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 CA.17: 5 residues within 4Å: Chain B: S.152, S.154, E.249, D.279, A.280 No protein-ligand interaction detected (PLIP)

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

NAG.18: 3 residues within 4Å: Chain B: N.403, S.416, N.417 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.403

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nguyen, A. et al., Structural and functional characterization of integrin alpha 5-targeting antibodies for anti-angiogenic therapy. Biorxiv (2025)

Release Date

2025-02-05

Peptides

Integrin alpha-5 light chain: A
Integrin beta-1: B
MINT1526A Fab Heavy Chain: C
MINT1526A Fab Light Chain: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
H

D
L

Integrin alpha-5 light chain

Integrin beta-1

MINT1526A Fab Heavy Chain

MINT1526A Fab Light Chain

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