SMTL ID : 1ji4.1

NAP protein from helicobacter pylori

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.52 Å

Oligo State

homo-12-mer

Ligands

12 x FE: FE (III) ION(Non-covalent)

FE.1: 6 residues within 4Å: Chain A: D.52, E.56 Chain D: H.25, H.37, Y.44 Ligands: UNX.11 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D Metal complexes: A:D.52, A:E.56, D:H.25 FE.4: 6 residues within 4Å: Chain B: D.52, E.56 Chain C: H.25, H.37, Y.44 Ligands: UNX.8 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Metal complexes: C:H.25, B:D.52, B:E.56 FE.7: 6 residues within 4Å: Chain B: H.25, H.37, Y.44 Chain C: D.52, E.56 Ligands: UNX.5 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Metal complexes: C:D.52, C:D.52, C:E.56, B:H.25 FE.10: 6 residues within 4Å: Chain A: H.25, H.37, Y.44 Chain D: D.52, E.56 Ligands: UNX.2 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain D Metal complexes: A:H.25, D:D.52, D:E.56 FE.13: 6 residues within 4Å: Chain E: D.52, E.56 Chain H: H.25, H.37, Y.44 Ligands: UNX.23 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain H Metal complexes: E:D.52, E:E.56, H:H.25 FE.16: 6 residues within 4Å: Chain F: D.52, E.56 Chain G: H.25, H.37, Y.44 Ligands: UNX.20 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain G Metal complexes: F:D.52, F:E.56, G:H.25 FE.19: 6 residues within 4Å: Chain F: H.25, H.37, Y.44 Chain G: D.52, E.56 Ligands: UNX.17 3 PLIP interactions: 2 interactions with chain G, 1 interactions with chain F Metal complexes: G:D.52, G:E.56, F:H.25 FE.22: 6 residues within 4Å: Chain E: H.25, H.37, Y.44 Chain H: D.52, E.56 Ligands: UNX.14 3 PLIP interactions: 2 interactions with chain H, 1 interactions with chain E Metal complexes: H:D.52, H:E.56, E:H.25 FE.25: 6 residues within 4Å: Chain I: D.52, E.56 Chain L: H.25, H.37, Y.44 Ligands: UNX.35 3 PLIP interactions: 2 interactions with chain I, 1 interactions with chain L Metal complexes: I:D.52, I:E.56, L:H.25 FE.28: 6 residues within 4Å: Chain J: D.52, E.56 Chain K: H.25, H.37, Y.44 Ligands: UNX.32 4 PLIP interactions: 3 interactions with chain J, 1 interactions with chain K Metal complexes: J:D.52, J:D.52, J:E.56, K:H.25 FE.31: 6 residues within 4Å: Chain J: H.25, H.37, Y.44 Chain K: D.52, E.56 Ligands: UNX.29 3 PLIP interactions: 2 interactions with chain K, 1 interactions with chain J Metal complexes: K:D.52, K:E.56, J:H.25 FE.34: 6 residues within 4Å: Chain I: H.25, H.37, Y.44 Chain L: D.52, E.56 Ligands: UNX.26 3 PLIP interactions: 2 interactions with chain L, 1 interactions with chain I Metal complexes: L:D.52, L:E.56, I:H.25

12 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.2: 4 residues within 4Å: Chain A: H.37 Chain D: E.56 Chain G: K.134 Ligands: FE.10 No protein-ligand interaction detected (PLIP) UNX.5: 4 residues within 4Å: Chain B: H.37 Chain C: E.56 Chain E: K.134 Ligands: FE.7 No protein-ligand interaction detected (PLIP) UNX.8: 4 residues within 4Å: Chain B: E.56 Chain C: H.37 Chain F: K.134 Ligands: FE.4 No protein-ligand interaction detected (PLIP) UNX.11: 4 residues within 4Å: Chain A: E.56 Chain D: H.37 Chain H: K.134 Ligands: FE.1 No protein-ligand interaction detected (PLIP) UNX.14: 4 residues within 4Å: Chain E: H.37 Chain H: E.56 Chain K: K.134 Ligands: FE.22 No protein-ligand interaction detected (PLIP) UNX.17: 4 residues within 4Å: Chain F: H.37 Chain G: E.56 Chain I: K.134 Ligands: FE.19 No protein-ligand interaction detected (PLIP) UNX.20: 4 residues within 4Å: Chain F: E.56 Chain G: H.37 Chain J: K.134 Ligands: FE.16 No protein-ligand interaction detected (PLIP) UNX.23: 4 residues within 4Å: Chain E: E.56 Chain H: H.37 Chain L: K.134 Ligands: FE.13 No protein-ligand interaction detected (PLIP) UNX.26: 4 residues within 4Å: Chain C: K.134 Chain I: H.37 Chain L: E.56 Ligands: FE.34 No protein-ligand interaction detected (PLIP) UNX.29: 4 residues within 4Å: Chain A: K.134 Chain J: H.37 Chain K: E.56 Ligands: FE.31 No protein-ligand interaction detected (PLIP) UNX.32: 4 residues within 4Å: Chain B: K.134 Chain J: E.56 Chain K: H.37 Ligands: FE.28 No protein-ligand interaction detected (PLIP) UNX.35: 4 residues within 4Å: Chain D: K.134 Chain I: E.56 Chain L: H.37 Ligands: FE.25 No protein-ligand interaction detected (PLIP)

12 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.3: 5 residues within 4Å: Chain A: E.46, Y.99, K.131, L.132, S.135 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:K.131, A:L.132 Hydrogen bonds: A:Y.99, A:S.135 Water bridges: A:S.135 MPD.6: 5 residues within 4Å: Chain B: E.46, Y.99, K.131, L.132, S.135 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:K.131, B:L.132 Hydrogen bonds: B:Y.99, B:S.135 Water bridges: B:S.135 MPD.9: 5 residues within 4Å: Chain C: E.46, Y.99, K.131, L.132, S.135 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:K.131, C:L.132 Hydrogen bonds: C:S.135 Water bridges: C:S.135 MPD.12: 5 residues within 4Å: Chain D: E.46, Y.99, K.131, L.132, S.135 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:K.131, D:L.132 Hydrogen bonds: D:S.135 Water bridges: D:S.135 MPD.15: 5 residues within 4Å: Chain E: E.46, Y.99, K.131, L.132, S.135 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:K.131, E:L.132 Hydrogen bonds: E:S.135 Water bridges: E:S.135 MPD.18: 5 residues within 4Å: Chain F: E.46, Y.99, K.131, L.132, S.135 5 PLIP interactions: 5 interactions with chain F Hydrophobic interactions: F:K.131, F:L.132 Hydrogen bonds: F:Y.99, F:S.135 Water bridges: F:S.135 MPD.21: 5 residues within 4Å: Chain G: E.46, Y.99, K.131, L.132, S.135 4 PLIP interactions: 4 interactions with chain G Hydrophobic interactions: G:K.131, G:L.132 Hydrogen bonds: G:Y.99, G:S.135 MPD.24: 5 residues within 4Å: Chain H: E.46, Y.99, K.131, L.132, S.135 4 PLIP interactions: 4 interactions with chain H Hydrophobic interactions: H:K.131, H:L.132 Hydrogen bonds: H:S.135 Water bridges: H:S.135 MPD.27: 5 residues within 4Å: Chain I: E.46, Y.99, K.131, L.132, S.135 5 PLIP interactions: 5 interactions with chain I Hydrophobic interactions: I:K.131, I:L.132 Hydrogen bonds: I:Y.99, I:S.135 Water bridges: I:S.135 MPD.30: 5 residues within 4Å: Chain J: E.46, Y.99, K.131, L.132, S.135 4 PLIP interactions: 4 interactions with chain J Hydrophobic interactions: J:K.131, J:L.132 Hydrogen bonds: J:S.135 Water bridges: J:S.135 MPD.33: 5 residues within 4Å: Chain K: E.46, Y.99, K.131, L.132, S.135 4 PLIP interactions: 4 interactions with chain K Hydrophobic interactions: K:K.131, K:L.132 Hydrogen bonds: K:S.135 Water bridges: K:S.135 MPD.36: 5 residues within 4Å: Chain L: E.46, Y.99, K.131, L.132, S.135 5 PLIP interactions: 5 interactions with chain L Hydrophobic interactions: L:K.131, L:L.132 Hydrogen bonds: L:Y.99, L:S.135 Water bridges: L:S.135

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zanotti, G. et al., Structure of the Neutrophil-activating Protein from Helicobacter pylori. J.Mol.Biol. (2002)

Release Date

2002-10-09

Peptides

NEUTROPHIL-ACTIVATING PROTEIN A: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

NEUTROPHIL-ACTIVATING PROTEIN A