SMTL ID : 7usl.1

Integrin alphaM/beta2 ectodomain in complex with adenylate cyclase toxin RTX751 and M1F5 Fab

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-mer

Ligands

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.1: 6 residues within 4Å: Chain A: Y.356, A.359, F.373, N.375, M.376, R.378 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.2: 5 residues within 4Å: Chain A: N.877, N.1059, V.1062 Chain C: L.378, F.379 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:V.1062, C:L.378 Hydrogen bonds: A:N.877, C:L.378

33 x CA: CALCIUM ION(Non-covalent)

CA.3: 5 residues within 4Å: Chain A: D.576, T.578, D.580, L.582, D.584 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.576, A:D.580, A:L.582, A:D.584, A:D.584 CA.4: 5 residues within 4Å: Chain A: D.513, N.515, D.517, L.519, D.521 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.517, A:L.519, A:D.521, A:D.521 CA.5: 5 residues within 4Å: Chain A: D.449, D.451, N.453, S.455, D.457 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.449, A:D.451, A:S.455, A:S.455, A:D.457 CA.15: 3 residues within 4Å: Chain B: S.116, D.120, E.325 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:S.116, B:E.325 CA.18: 7 residues within 4Å: Chain C: D.134, G.135, A.137, G.167, D.169, G.170, D.172 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:A.137, C:G.167, C:D.172 CA.19: 5 residues within 4Å: Chain C: G.170, D.172, G.185, A.187, N.190 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:G.170, C:D.172, C:G.185, C:A.187 CA.20: 7 residues within 4Å: Chain C: G.270, A.271, G.272, D.274, G.287, S.289, D.292 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:G.270, C:D.274, C:G.287, C:S.289, C:D.292 CA.21: 7 residues within 4Å: Chain C: N.279, H.281, N.283, G.296, G.297, A.298, D.301 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:N.279, C:H.281, C:G.296, C:A.298, C:D.301 CA.22: 7 residues within 4Å: Chain C: G.288, G.290, D.292, G.305, G.306, E.307, N.310 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:G.288, C:G.290, C:D.292, C:G.305, C:E.307 CA.23: 8 residues within 4Å: Chain C: G.297, A.298, G.299, D.301, G.314, G.315, A.316, D.319 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:G.297, C:G.299, C:D.301, C:G.314, C:D.319 CA.24: 8 residues within 4Å: Chain C: G.315, A.316, G.317, D.319, G.334, G.335, A.336, D.339 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:G.317, C:D.319, C:G.334, C:A.336, C:D.339 CA.25: 6 residues within 4Å: Chain C: G.335, A.336, G.337, D.339, N.386, E.388 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:G.335, C:G.337, C:D.339, C:N.386, C:E.388 CA.26: 6 residues within 4Å: Chain C: S.393, L.395, D.397, G.410, D.412, D.415 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:L.395, C:G.410, C:D.412, C:D.415, C:D.415 CA.27: 6 residues within 4Å: Chain C: D.402, Q.404, N.406, G.419, G.421, D.424 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.402, C:Q.404, C:G.419, C:G.421, C:D.424 CA.28: 7 residues within 4Å: Chain C: H.411, G.413, D.415, G.428, G.429, L.430, D.433 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:H.411, C:G.413, C:D.415, C:G.428, C:D.433 CA.29: 7 residues within 4Å: Chain C: R.420, G.421, G.422, D.424, G.437, D.439, D.442 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:G.422, C:D.424, C:G.437, C:D.439, C:D.442 CA.30: 5 residues within 4Å: Chain C: G.429, G.431, D.433, E.449, D.453 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:G.429, C:G.431, C:D.433, C:E.449, C:D.453 CA.31: 7 residues within 4Å: Chain C: E.438, D.439, G.440, D.442, G.457, A.459, D.462 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:E.438, C:D.442, C:G.457, C:A.459, C:D.462 CA.32: 5 residues within 4Å: Chain C: G.458, G.460, D.462, N.510, E.512 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:G.458, C:G.460, C:D.462, C:N.510, C:E.512 CA.33: 6 residues within 4Å: Chain C: T.517, M.519, D.521, G.534, G.536, D.539 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:T.517, C:M.519, C:D.521, C:G.534, C:D.539 CA.34: 7 residues within 4Å: Chain C: D.526, Q.528, N.530, G.543, G.544, D.545, D.548 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.526, C:Q.528, C:G.543, C:D.545, C:D.548 CA.35: 8 residues within 4Å: Chain C: Q.535, G.536, G.537, D.539, G.552, G.553, D.554, D.557 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:Q.535, C:G.537, C:D.539, C:G.552, C:D.557 CA.36: 7 residues within 4Å: Chain C: G.544, D.545, G.546, D.548, G.561, A.563, D.566 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:G.544, C:G.546, C:D.548, C:G.561, C:D.566 CA.37: 6 residues within 4Å: Chain C: G.553, G.555, D.557, G.570, L.572, D.575 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:G.553, C:G.555, C:D.557, C:G.570, C:D.575 CA.38: 7 residues within 4Å: Chain C: D.562, A.563, G.564, D.566, G.579, A.581, D.584 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:G.564, C:D.566, C:G.579, C:A.581, C:D.584 CA.39: 5 residues within 4Å: Chain C: G.571, G.573, D.575, E.593, D.595 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:G.571, C:G.573, C:E.593, C:D.595 CA.40: 6 residues within 4Å: Chain C: G.599, G.600, G.602, D.604, G.651, E.653 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:G.600, C:G.602, C:G.651, C:E.653 CA.41: 7 residues within 4Å: Chain C: T.658, L.660, D.662, G.675, A.676, G.677, D.680 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:L.660, C:G.675, C:G.677, C:D.680, C:D.680 CA.42: 6 residues within 4Å: Chain C: D.667, Q.669, N.671, G.684, E.686, D.689 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.667, C:Q.669, C:G.684, C:E.686, C:D.689 CA.43: 7 residues within 4Å: Chain C: A.676, G.677, G.678, D.680, G.693, D.695, D.698 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:G.678, C:D.680, C:G.693, C:D.695, C:D.698 CA.44: 7 residues within 4Å: Chain C: G.684, G.685, E.686, G.687, D.689, A.704, D.707 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:G.685, C:G.687, C:D.689, C:A.704, C:D.707 CA.45: 8 residues within 4Å: Chain C: G.694, D.695, G.696, D.698, G.711, E.712, A.713, D.716 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:G.694, C:G.696, C:D.698, C:G.711, C:D.716 CA.46: 8 residues within 4Å: Chain C: E.712, A.713, G.714, D.716, G.731, G.732, D.733, D.736 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:E.712, C:G.714, C:G.731, C:D.733, C:D.736

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

NAG.6: 2 residues within 4Å: Chain A: N.70, T.96 No protein-ligand interaction detected (PLIP) NAG.7: 3 residues within 4Å: Chain A: T.678, N.680, T.682 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.682 NAG.8: 6 residues within 4Å: Chain A: T.659, Y.660, D.661, N.718, F.719, S.720 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.659 Hydrogen bonds: A:N.718 NAG.9: 4 residues within 4Å: Chain A: E.783, N.785, K.814, N.864 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.814, A:K.814 NAG.10: 6 residues within 4Å: Chain A: F.805, K.882, N.884, V.885, T.886, R.893 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.884, A:R.893 NAG.11: 3 residues within 4Å: Chain A: N.924, T.926, P.1083 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.924 NAG.12: 4 residues within 4Å: Chain A: A.1001, V.1003, N.1005, S.1007 No protein-ligand interaction detected (PLIP) NAG.13: 5 residues within 4Å: Chain A: H.916, Q.938, E.1026, F.1027, N.1028 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:E.1026 Hydrogen bonds: A:Q.938, A:N.1028 NAG.14: 2 residues within 4Å: Chain A: S.932, N.1034 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.932 NAG.16: 1 residues within 4Å: Chain B: N.190 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.190 NAG.17: 1 residues within 4Å: Chain B: N.232 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Goldsmith, J.A. et al., Structural basis for non-canonical integrin engagement by Bordetella adenylate cyclase toxin. Cell Rep (2022)

Release Date

2022-08-17

Peptides

Integrin alpha-M: A
Integrin beta: B
Bifunctional hemolysin-adenylate cyclase: C
M1F5 fab heavy chain: D
M1F5 fab light chain: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
H

E
L

Integrin alpha-M

Integrin beta

Bifunctional hemolysin-adenylate cyclase

M1F5 fab heavy chain

M1F5 fab light chain

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