SMTL ID : 3v4v.2 (1 other biounit)

crystal structure of a4b7 headpiece complexed with Fab ACT-1 and RO0505376

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

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(Non-covalent)

NAG-NAG-BMA-MAN.1: 5 residues within 4Å: Chain A: D.176, L.177, N.196, T.198, T.199 No protein-ligand interaction detected (PLIP)

5 x CA: CALCIUM ION(Non-covalent)

CA.2: 6 residues within 4Å: Chain A: D.281, N.283, D.285, F.287, S.288, D.289 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.285, A:F.287 CA.3: 5 residues within 4Å: Chain A: D.344, D.346, D.348, F.350, D.352 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.344, A:D.346, A:F.350 CA.4: 6 residues within 4Å: Chain A: D.406, D.408, N.410, Y.412, D.414, T.430 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.408, A:Y.412, H2O.1 CA.10: 4 residues within 4Å: Chain B: S.144, D.147, D.148, E.354 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:S.144, B:E.354 CA.11: 6 residues within 4Å: Chain B: D.179, N.235, D.237, S.238, P.239, E.240 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.179, B:D.237

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

NAG.5: 6 residues within 4Å: Chain A: N.46, S.48, V.49, P.76, N.77, R.89 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.89 NAG.6: 3 residues within 4Å: Chain A: G.29, E.104, N.105 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.104 NAG.7: 4 residues within 4Å: Chain A: S.445, N.447, T.449, K.450 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:T.449 Hydrogen bonds: A:S.445, A:N.447, A:K.450, A:K.450 NAG.8: 6 residues within 4Å: Chain A: F.483, N.485, S.487, A.547, Y.548, H.549 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.487, A:H.549 NAG.12: 3 residues within 4Å: Chain B: N.260, S.444, E.446 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:N.260 Hydrogen bonds: B:S.444, B:E.446

1 x MG: MAGNESIUM ION(Non-covalent)

MG.9: 5 residues within 4Å: Chain B: S.142, S.144, E.240, D.270 Ligands: 0DU.13 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.142, B:S.144, B:E.240, H2O.1, H2O.1

1 x 0DU: N-(2,6-dichlorobenzoyl)-4-[1,6-dimethyl-2-oxo-4-(trifluoromethyl)-1,2-dihydropyridin-3-yl]-L-phenylalanine(Non-covalent)

0DU.13: 13 residues within 4Å: Chain A: Y.187, F.214 Chain B: S.142, Y.143, S.144, P.196, P.198, G.234, N.235, L.236, D.237, S.238 Ligands: MG.9 9 PLIP interactions: 3 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:Y.187, A:F.214, B:L.236 pi-Stacking: A:Y.187 Hydrogen bonds: B:Y.143, B:S.144, B:N.235, B:N.235, B:S.238

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yu, Y. et al., Structural specializations of a4b7, an Integrin that Mediates Rolling Adhesion. J.Cell Biol. (2012)

Release Date

2012-01-11

Peptides

Integrin alpha-4: A
Integrin beta-7: B
MONOCLONAL ANTIBODY Act-1 HEAVY CHAIN: C
MONOCLONAL ANTIBODY Act-1 LIGHT CHAIN: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
M

D
N

Integrin alpha-4

Integrin beta-7

MONOCLONAL ANTIBODY Act-1 HEAVY CHAIN

MONOCLONAL ANTIBODY Act-1 LIGHT CHAIN

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