SMTL ID : 2gk2.3 (4 other biounits)

Crystal structure of the N terminal domain of human CEACAM1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-hexamer

Ligands

6 x NI: NICKEL (II) ION(Non-covalent)

NI.1: 8 residues within 4Å: Chain A: H.109, V.110 Chain B: H.109, V.110 Chain C: H.109, V.110 Ligands: NI.4, NI.7 6 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:H.109, C:H.109, B:H.109, H2O.1, H2O.2, H2O.4 NI.4: 8 residues within 4Å: Chain A: H.109, V.110 Chain B: H.109, V.110 Chain C: H.109, V.110 Ligands: NI.1, NI.7 6 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:H.109, C:H.109, B:H.109, H2O.1, H2O.2, H2O.4 NI.7: 8 residues within 4Å: Chain A: H.109, V.110 Chain B: H.109, V.110 Chain C: H.109, V.110 Ligands: NI.1, NI.4 6 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:H.109, C:H.109, B:H.109, H2O.1, H2O.2, H2O.4 NI.10: 1 residues within 4Å: Chain D: H.109 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:H.109 NI.12: 1 residues within 4Å: Chain E: H.109 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:H.109 NI.14: 1 residues within 4Å: Chain F: H.109 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:H.109

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: V.25, H.26, N.27, L.28 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.27, A:L.28 Water bridges: A:V.25, A:H.26 GOL.3: 7 residues within 4Å: Chain A: K.39, G.40, R.47, T.87, G.88, F.89 Chain B: F.13 10 PLIP interactions: 3 interactions with chain B, 7 interactions with chain A Water bridges: B:E.9, B:F.13, B:F.13, A:E.41, A:N.85 Hydrogen bonds: A:K.39, A:R.47, A:R.47, A:F.89, A:F.89 GOL.5: 4 residues within 4Å: Chain B: V.25, H.26, N.27, L.28 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.27, B:L.28 Water bridges: B:V.25, B:H.26 GOL.6: 7 residues within 4Å: Chain B: K.39, G.40, R.47, T.87, G.88, F.89 Chain C: F.13 10 PLIP interactions: 3 interactions with chain C, 7 interactions with chain B Water bridges: C:E.9, C:F.13, C:F.13, B:E.41, B:N.85 Hydrogen bonds: B:K.39, B:R.47, B:R.47, B:F.89, B:F.89 GOL.8: 4 residues within 4Å: Chain C: V.25, H.26, N.27, L.28 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.27, C:L.28 Water bridges: C:V.25, C:H.26 GOL.9: 7 residues within 4Å: Chain A: F.13 Chain C: K.39, G.40, R.47, T.87, G.88, F.89 10 PLIP interactions: 7 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:K.39, C:R.47, C:R.47, C:F.89, C:F.89 Water bridges: C:E.41, C:N.85, A:E.9, A:F.13, A:F.13 GOL.11: 3 residues within 4Å: Chain D: Y.72, P.73, N.74 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.74, D:N.74 GOL.13: 3 residues within 4Å: Chain E: Y.72, P.73, N.74 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.74, E:N.74 GOL.15: 3 residues within 4Å: Chain F: Y.72, P.73, N.74 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:N.74, F:N.74

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fedarovich, A. et al., Structure of the N-terminal domain of human CEACAM1: binding target of the opacity proteins during invasion of Neisseria meningitidis and N. gonorrhoeae. Acta Crystallogr.,Sect.D (2006)

Release Date

2006-09-05

Peptides

Carcinoembryonic antigen-related cell adhesion molecule 1: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
B

E
B

F
B

Carcinoembryonic antigen-related cell adhesion molecule 1

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