SMTL ID : 3v6o.1 (1 other biounit)

Leptin Receptor-antibody complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x CYS: CYSTEINE(Non-covalent)

CYS.1: 2 residues within 4Å: Chain A: C.177 Ligands: EDO.3 2 PLIP interactions: 2 Ligand-Ligand interactions Hydrogen bonds: C.1, C.1

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

EDO.2: 2 residues within 4Å: Chain A: K.59, D.60 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.60, A:D.60 Water bridges: A:Y.39, A:Y.39, A:K.59, A:K.59 EDO.3: 1 residues within 4Å: Ligands: CYS.1 1 PLIP interactions: 1 Ligand-Ligand interactions Hydrogen bonds: C.1 EDO.4: 2 residues within 4Å: Chain A: C.46, D.48 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:C.46 EDO.5: 3 residues within 4Å: Chain A: D.175, C.177, A.178 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.175 EDO.6: 3 residues within 4Å: Chain A: S.106, G.193, Y.194 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.106 EDO.7: 5 residues within 4Å: Chain A: K.59, D.60, C.61, Y.62 Ligands: EDO.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.60, A:C.61, A:C.61 EDO.8: 5 residues within 4Å: Chain A: W.22, L.35, C.61, Y.69 Ligands: EDO.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:C.61 EDO.9: 6 residues within 4Å: Chain A: S.8, C.9, E.10, T.19, R.21, Y.194 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.10, A:E.10, A:T.19 EDO.12: 8 residues within 4Å: Chain B: Q.40, K.44, G.45, L.46 Chain C: D.86, F.88, G.100, S.101 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:Q.40, B:K.44, B:L.46, C:G.100 Water bridges: B:K.44 EDO.13: 6 residues within 4Å: Chain B: P.42, T.91, A.92, M.93, V.114, T.115 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.115 Water bridges: B:S.113, B:E.153 EDO.16: 5 residues within 4Å: Chain C: I.145, N.146, V.147, N.162, W.164 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:N.146, C:V.147, C:V.147 Water bridges: C:I.145, C:I.145 EDO.17: 5 residues within 4Å: Chain C: Q.38, Q.46, L.48, P.60, F.63 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Q.38, C:K.40, C:Q.46 EDO.18: 4 residues within 4Å: Chain C: F.50, R.55, T.57 Ligands: ACT.15 1 PLIP interactions: 1 interactions with chain C Water bridges: C:T.57

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.10: 7 residues within 4Å: Chain A: R.41, F.77 Chain B: D.33, K.98, D.100, D.106 Ligands: ACT.11 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:D.100, B:G.101, B:D.106 Salt bridges: B:K.98, A:R.41 Hydrophobic interactions: A:F.77 Water bridges: A:R.41 ACT.11: 5 residues within 4Å: Chain B: D.100, D.106, Y.107 Ligands: ACT.10, ACT.15 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.106 Salt bridges: B:K.98 ACT.15: 8 residues within 4Å: Chain B: D.100, T.104, D.106 Chain C: F.50, H.56, T.57 Ligands: ACT.11, EDO.18 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:F.50, B:T.104 Hydrogen bonds: C:T.57 Water bridges: C:T.57 Salt bridges: C:H.56

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

NA.14: 3 residues within 4Å: Chain B: S.190, W.193, P.194 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.190

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Carpenter, B. et al., Structure of the human obesity receptor leptin-binding domain reveals the mechanism of leptin antagonism by a monoclonal antibody. Structure (2012)

Release Date

2012-03-14

Peptides

Leptin receptor: A
Monoclonal antibody 9F8 fab fragment Heavy chain: B
Monoclonal antibody 9F8 fab fragment Light chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
E

Leptin receptor

Monoclonal antibody 9F8 fab fragment Heavy chain

Monoclonal antibody 9F8 fab fragment Light chain

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