SMTL ID : 4irz.1

Crystal structure of A4b7 headpiece complexed with Fab Natalizumab

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.84 Å

Oligo State

hetero-1-1-1-mer

Ligands

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(Non-covalent)

NAG-NAG-BMA.1: 9 residues within 4Å: Chain A: D.176, L.177, N.196, T.198, T.199, H.231, T.233, I.253 Chain C: N.55 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.231

3 x CA: CALCIUM ION(Non-covalent)

CA.2: 7 residues within 4Å: Chain A: D.281, L.282, N.283, D.285, F.287, S.288, D.289 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.281, A:D.285, A:F.287, A:D.289, H2O.1 CA.3: 7 residues within 4Å: Chain A: D.344, D.346, D.348, F.350, D.352, N.371, G.372 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.344, A:D.346, A:D.348, A:D.352, H2O.1 CA.4: 7 residues within 4Å: Chain A: D.406, A.407, D.408, N.410, Y.412, D.414, T.430 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.406, A:D.408, A:Y.412, A:D.414, H2O.1

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

NAG.5: 7 residues within 4Å: Chain A: N.46, S.48, V.49, P.76, N.77, G.78, R.89 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.46, A:R.89, A:R.89 NAG.6: 4 residues within 4Å: Chain A: H.28, G.29, E.104, N.105 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.104, A:N.105, A:N.105 NAG.7: 6 residues within 4Å: Chain A: N.485, S.487, V.510, A.547, Y.548, H.549 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.510 Hydrogen bonds: A:N.485, A:N.485 NAG.8: 5 residues within 4Å: Chain A: N.505, S.508, V.510, I.511, T.512 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.505, A:S.508, A:T.512, A:T.512, A:T.512

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.9: 8 residues within 4Å: Chain A: Y.21, W.93, V.96, H.113, R.114, I.169, Y.220 Ligands: NDS.10 No protein-ligand interaction detected (PLIP)

1 x NDS: ETHYL DIMETHYL AMMONIO PROPANE SULFONATE(Non-covalent)

NDS.10: 13 residues within 4Å: Chain A: Y.21, V.96, T.97, L.98, I.169, S.170, S.171, F.172, Y.220, S.221, V.222, Q.399 Ligands: PEG.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.21

1 x NA: SODIUM ION(Non-functional Binders)

NA.11: 5 residues within 4Å: Chain C: K.63, F.64, Q.65, G.66, R.67 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:F.64, C:R.67

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yu, Y. et al., How natalizumab binds and antagonizes alpha 4 integrins. J.Biol.Chem. (2013)

Release Date

2013-09-25

Peptides

Integrin alpha4 subunit: A
Fab Natalizumab light chain: B
Fab Natalizumab heavy chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
L

C
H

Integrin alpha4 subunit

Fab Natalizumab light chain

Fab Natalizumab heavy chain

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