SMTL ID : 2qqm.1

Crystal Structure of the a2b1b2 Domains from Human Neuropilin-1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x NAG- FUC- NAG- FUC: alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-FUC-NAG-FUC.1: 5 residues within 4Å: Chain A: I.50, E.52, N.125, Y.126, S.127 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 4 residues within 4Å: Chain A: S.12, N.14, F.42, F.81 No protein-ligand interaction detected (PLIP)

1 x CA: CALCIUM ION(Non-covalent)

CA.3: 5 residues within 4Å: Chain A: E.59, D.73, D.114, A.116, I.117 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.59, A:D.73, A:A.116, A:I.117, H2O.2

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

EDO.4: 4 residues within 4Å: Chain A: S.343, Y.344, K.380, E.431 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.344 EDO.5: 3 residues within 4Å: Chain A: I.100, R.101, G.195 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.101, A:G.195 EDO.6: 5 residues within 4Å: Chain A: I.236, K.237, L.263, N.409, T.412 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.235, A:K.237, A:N.409 EDO.7: 5 residues within 4Å: Chain A: R.101, L.143, E.149, L.194, R.198 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.149, A:R.198 EDO.8: 4 residues within 4Å: Chain A: N.173, Q.206, T.252, R.282 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.252, A:R.282, A:R.282 EDO.9: 5 residues within 4Å: Chain A: E.141, A.142, L.143, K.289, D.292 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.289, A:D.292 Water bridges: A:K.289

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Appleton, B.A. et al., Structural studies of neuropilin/antibody complexes provide insights into semaphorin and VEGF binding. Embo J. (2007)

Release Date

2007-11-20

Peptides

Neuropilin-1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Neuropilin-1