SMTL ID : 5dq0.1

Structure of human neuropilin-2 b1 domain with novel and unique zinc binding site

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: Y.104, H.106, H.128 Ligands: CL.5 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:Y.104, A:H.106, A:H.128 ZN.2: 3 residues within 4Å: Chain A: E.13, H.41 Ligands: CL.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.13, A:E.13, A:H.41 ZN.3: 1 residues within 4Å: Chain A: E.99 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.99, A:E.99, H2O.5

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

CL.4: 3 residues within 4Å: Chain A: E.13, H.41 Ligands: ZN.2 Ligand excluded by PLIP CL.5: 5 residues within 4Å: Chain A: Y.104, H.106, L.127, H.128 Ligands: ZN.1 Ligand excluded by PLIP

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

EDO.6: 2 residues within 4Å: Chain A: H.106, H.128 1 PLIP interactions: 1 interactions with chain A Water bridges: A:G.107 EDO.7: 2 residues within 4Å: Chain A: H.106, K.111 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.111, A:K.111

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.8: 6 residues within 4Å: Chain A: W.33, D.52, S.78, T.81, N.83, Y.85 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.78, A:N.83, A:Y.85, A:Y.85 pi-Cation interactions: A:Y.28

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tsai, Y.I. et al., Structure of human neuropilin-2 b1 domain with novel and unique zinc binding site. To Be Published

Release Date

2016-09-28

Peptides

Neuropilin-2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Neuropilin-2

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