SMTL ID : 4qaf.1

Crystal structure of an engineered lipocalin (Anticalin) in complex with VEGF(8-109)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-2-2-mer

Ligands

2 x OMA: 10-{(1R,2R)-2-[(2E)-hex-2-en-1-yl]cyclopropyl}decanoic acid(Non-covalent)

OMA.1: 13 residues within 4Å: Chain A: V.9, M.18, V.20, V.22, L.25, L.28, V.32, M.51, I.53, V.60, A.62, Y.93, V.109 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:V.9, A:V.20, A:V.22, A:L.25, A:L.28, A:V.32, A:V.60, A:A.62, A:Y.93, A:V.109, A:V.109 OMA.6: 10 residues within 4Å: Chain D: V.9, M.18, V.20, L.25, L.28, A.62, V.81, F.95, V.109, L.111 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:V.9, D:V.20, D:V.20, D:V.20, D:L.25, D:L.28, D:A.62, D:V.81, D:F.95, D:F.95, D:V.109, D:L.111, D:L.111

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 5 residues within 4Å: Chain B: Y.38, R.75, K.77, H.83 Chain D: P.105 5 PLIP interactions: 5 interactions with chain B Water bridges: B:Y.38, B:Y.38 Salt bridges: B:R.75, B:K.77, B:H.83 SO4.3: 5 residues within 4Å: Chain A: S.87, H.88 Chain B: Y.18, E.96, C.97 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.18, B:C.97 Water bridges: B:C.95 Salt bridges: B:K.94, A:H.88 SO4.4: 5 residues within 4Å: Chain A: P.105 Chain C: Y.38, R.75, K.77, H.83 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:Y.38, C:Y.38 Water bridges: C:K.77, C:K.77 Salt bridges: C:R.75, C:K.77, C:H.83

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

ACT.5: 8 residues within 4Å: Chain A: G.108, W.110 Chain C: I.76, K.77, P.78, H.79, G.81, Q.82 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:W.110 Water bridges: A:G.108, A:G.108 Hydrophobic interactions: C:I.76

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Giese, T. et al., Crystal structure of an Anticalin with specific blocking activity towards human vascular endothelial growth factor (VEGF) reveals plasticity of the lipocalin fold. To be Published

Release Date

2015-05-06

Peptides

Lipocalin-1: AD
Vascular endothelial growth factor A: BC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
B

B
C

C
D

Lipocalin-1

Vascular endothelial growth factor A