SMTL ID : 4e6r.1

Crystal structure of a Cytoplasmic protein NCK2 (NCK2) from Homo sapiens at 2.20 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

10 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: E.30 Chain B: E.15 Chain D: D.34 Ligands: IMD.4 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 1 interactions with chain D Metal complexes: A:E.30, A:E.30, B:E.15, D:D.34 ZN.2: 1 residues within 4Å: Chain A: E.13 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.13, A:E.13, H2O.1, H2O.1, H2O.1 ZN.3: 2 residues within 4Å: Chain A: E.56, D.58 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.56, A:D.58 ZN.5: 4 residues within 4Å: Chain A: E.15 Chain B: E.30 Chain C: D.34 Ligands: IMD.7 4 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B, 1 interactions with chain C Metal complexes: A:E.15, B:E.30, B:E.30, C:D.34 ZN.9: 1 residues within 4Å: Chain B: E.13 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.13, B:E.13, H2O.1, H2O.2, H2O.2 ZN.10: 4 residues within 4Å: Chain B: D.34 Chain C: E.30 Chain D: E.15 Ligands: IMD.13 4 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C, 1 interactions with chain D Metal complexes: B:D.34, C:E.30, C:E.30, D:E.15 ZN.11: 1 residues within 4Å: Chain C: E.13 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:E.13, C:E.13, H2O.2, H2O.2, H2O.2 ZN.12: 2 residues within 4Å: Chain C: E.56, D.58 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.56, C:D.58 ZN.14: 4 residues within 4Å: Chain A: D.34 Chain C: E.15 Chain D: E.30 Ligands: IMD.16 4 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D, 1 interactions with chain A Metal complexes: C:E.15, D:E.30, D:E.30, A:D.34 ZN.18: 1 residues within 4Å: Chain D: E.13 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:E.13, D:E.13, H2O.2, H2O.3, H2O.3

4 x IMD: IMIDAZOLE(Non-covalent)

IMD.4: 8 residues within 4Å: Chain A: E.30 Chain B: E.15 Chain D: C.32, D.34, W.36, W.47 Ligands: ZN.1, UNL.17 1 PLIP interactions: 1 interactions with chain D pi-Stacking: D:W.47 IMD.7: 10 residues within 4Å: Chain A: E.15 Chain B: E.30, W.47 Chain C: C.32, D.34, W.36, W.47 Ligands: ZN.5, UNL.8, UNL.15 1 PLIP interactions: 1 interactions with chain C pi-Stacking: C:W.47 IMD.13: 8 residues within 4Å: Chain B: C.32, D.34, W.36, W.47 Chain C: E.30 Chain D: E.15 Ligands: UNL.8, ZN.10 1 PLIP interactions: 1 interactions with chain B pi-Stacking: B:W.47 IMD.16: 10 residues within 4Å: Chain A: C.32, D.34, W.36, W.47 Chain C: E.15 Chain D: E.30, W.47 Ligands: UNL.6, ZN.14, UNL.17 1 PLIP interactions: 1 interactions with chain A pi-Stacking: A:W.47

4 x UNL: UNKNOWN LIGAND

UNL.6: 10 residues within 4Å: Chain A: R.14, D.16, E.17, W.36, W.47 Chain C: R.14, E.15 Ligands: UNL.15, IMD.16, UNL.17 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:D.16, A:W.47, C:E.15, C:E.15, C:E.15 UNL.8: 11 residues within 4Å: Chain B: R.14, D.16, E.17, W.36, W.47 Chain D: R.14, E.15 Ligands: IMD.7, IMD.13, UNL.15, UNL.17 5 PLIP interactions: 1 interactions with chain D, 4 interactions with chain B Hydrogen bonds: D:E.15, B:D.16, B:D.16, B:E.17, B:E.17 UNL.15: 10 residues within 4Å: Chain A: R.14, E.15 Chain C: R.14, D.16, E.17, W.36, W.47 Ligands: UNL.6, IMD.7, UNL.8 10 PLIP interactions: 5 interactions with chain C, 5 interactions with chain A Hydrogen bonds: C:D.16, C:D.16, C:E.17, C:W.36, C:W.47, A:R.14, A:E.15, A:E.15, A:E.15, A:E.15 UNL.17: 11 residues within 4Å: Chain B: R.14, E.15 Chain D: R.14, D.16, E.17, W.36, W.47 Ligands: IMD.4, UNL.6, UNL.8, IMD.16 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain D Hydrogen bonds: B:R.14, B:E.15, B:E.15, D:D.16, D:E.17, D:W.36

Links

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Citation

Joint Center for Structural Genomics (JCSG) et al., Crystal structure of a Cytoplasmic protein NCK2 (NCK2) from Homo sapiens at 2.20 A resolution. To be published

Release Date

2012-04-04

Peptides

Cytoplasmic protein NCK2: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Cytoplasmic protein NCK2