SMTL ID : 3qa3.1 (3 other biounits)

Crystal Structure of A-domain in complex with antibody

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

hetero-1-1-1-mer

Ligands

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 6 residues within 4Å: Chain A: L.102, T.103, F.104 Chain B: L.45, E.46, W.47 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:W.47, A:F.104, A:F.104 EDO.2: 7 residues within 4Å: Chain A: N.144, D.173, K.175, D.176 Chain B: G.171, V.172, H.173 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:H.173, A:N.144 EDO.4: 9 residues within 4Å: Chain B: E.99, H.101, Y.102, G.103, Y.104, G.106 Chain C: G.12, L.75, G.76 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:E.99, B:H.101, B:G.103, B:Y.104, B:G.106, C:G.12, C:G.76 EDO.5: 2 residues within 4Å: Chain B: D.56, A.72 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.56

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain B: K.38, R.40, E.46, K.63, E.89, D.90 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.38, B:R.40, B:E.46 GOL.7: 6 residues within 4Å: Chain A: Y.100 Chain B: K.59 Chain C: E.47, H.79, G.116, P.118 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:Y.100, A:Y.100, C:E.47 GOL.8: 6 residues within 4Å: Chain B: K.57 Chain C: F.49, R.50, I.51, K.86, E.90 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:I.51, B:K.57

1 x CA: CALCIUM ION(Non-covalent)

CA.6: 5 residues within 4Å: Chain B: D.105 Chain C: S.11, S.13, T.78, D.111 5 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: C:S.11, C:D.111, B:D.105, H2O.1, H2O.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mahalingam, B. et al., Stable Coordination of the Inhibitory Ca2+ Ion at the Metal Ion-Dependent Adhesion Site in Integrin CD11b/CD18 by an Antibody-Derived Ligand Aspartate: Implications for Integrin Regulation and Structure-Based Drug Design. J.Immunol. (2011)

Release Date

2011-11-30

Peptides

Antibody Light chain: A
Antibody Heavy chain: B
Integrin alpha-M: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
G

Antibody Light chain

Antibody Heavy chain

Integrin alpha-M

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