SMTL ID : 3q3g.4 (3 other biounits)

Crystal Structure of A-domain in complex with antibody

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

EDO.1: 2 residues within 4Å: Chain A: S.128, E.129 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.128 EDO.2: 3 residues within 4Å: Chain A: D.1, Q.27, S.99 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.1, A:S.99, A:S.99 Water bridges: A:I.2 EDO.5: 3 residues within 4Å: Chain A: E.129 Chain B: V.130, K.217 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.130, B:K.217 EDO.6: 3 residues within 4Å: Chain B: G.8, A.9, E.10 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.8, B:A.9 EDO.7: 6 residues within 4Å: Chain A: S.122 Chain B: Q.140, M.144, V.145, T.146, T.191 No protein-ligand interaction detected (PLIP) EDO.8: 5 residues within 4Å: Chain B: F.64, Q.65, G.66, A.68, T.69 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.65, B:G.66 EDO.13: 6 residues within 4Å: Chain A: S.32 Chain C: D.142, A.143, F.144, R.145, S.146 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:D.142, C:R.145, C:S.146, C:S.146 EDO.14: 6 residues within 4Å: Chain C: V.88, R.89, F.92, N.93, K.104, E.131 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:V.88, C:N.93, C:K.104 Water bridges: C:I.94

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 8 residues within 4Å: Chain A: S.9, V.91, Y.93, A.106, G.107, K.109 Chain B: Q.43, G.44 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.9, A:A.106, A:K.109 GOL.9: 2 residues within 4Å: Chain B: Q.65, G.66 No protein-ligand interaction detected (PLIP) GOL.10: 6 residues within 4Å: Chain B: Q.5, Q.6, S.7, S.21, C.22, T.23 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.21, B:T.23, B:T.23, B:T.23

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 3 residues within 4Å: Chain A: S.182, T.184 Chain B: S.187 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain B: Q.114, G.115 Ligand excluded by PLIP

1 x CA: CALCIUM ION(Non-covalent)

CA.12: 5 residues within 4Å: Chain B: D.105 Chain C: S.11, S.13, T.78, D.111 5 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: B:D.105, C:S.11, C:D.111, H2O.1, H2O.3

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
J

B
K

C
L

Antibody Light Chain

Antibody Heavy chain

Integrin alpha-M

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