SMTL ID : 4evc.1

Crystal Structure HP-NAP from strain YS39 cadmium loaded (Cocrystallization 50mM)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-12-mer

Ligands

156 x CD: CADMIUM ION(Non-covalent)

CD.1: 3 residues within 4Å: Chain A: H.45 Chain J: D.72, E.76 Ligand excluded by PLIP CD.2: 1 residues within 4Å: Chain A: H.57 Ligand excluded by PLIP CD.3: 1 residues within 4Å: Chain A: H.121 Ligand excluded by PLIP CD.4: 2 residues within 4Å: Chain A: E.114, E.117 Ligand excluded by PLIP CD.5: 2 residues within 4Å: Chain A: D.69, D.73 Ligand excluded by PLIP CD.6: 2 residues within 4Å: Chain A: E.25, H.29 Ligand excluded by PLIP CD.7: 2 residues within 4Å: Chain A: A.164 Chain E: H.107 Ligand excluded by PLIP CD.8: 3 residues within 4Å: Chain A: E.61, E.62, E.65 Ligand excluded by PLIP CD.9: 2 residues within 4Å: Chain A: E.125, E.128 Ligand excluded by PLIP CD.10: 2 residues within 4Å: Chain A: H.107, D.110 Ligand excluded by PLIP CD.11: 1 residues within 4Å: Chain A: H.83 Ligand excluded by PLIP CD.12: 1 residues within 4Å: Chain A: H.83 Ligand excluded by PLIP CD.13: 1 residues within 4Å: Chain A: H.84 Ligand excluded by PLIP CD.14: 3 residues within 4Å: Chain B: H.45 Chain E: D.72, E.76 Ligand excluded by PLIP CD.15: 1 residues within 4Å: Chain B: H.57 Ligand excluded by PLIP CD.16: 1 residues within 4Å: Chain B: H.121 Ligand excluded by PLIP CD.17: 2 residues within 4Å: Chain B: E.114, E.117 Ligand excluded by PLIP CD.18: 2 residues within 4Å: Chain B: D.69, D.73 Ligand excluded by PLIP CD.19: 2 residues within 4Å: Chain B: E.25, H.29 Ligand excluded by PLIP CD.20: 2 residues within 4Å: Chain B: A.164 Chain I: H.107 Ligand excluded by PLIP CD.21: 3 residues within 4Å: Chain B: E.61, E.62, E.65 Ligand excluded by PLIP CD.22: 2 residues within 4Å: Chain B: E.125, E.128 Ligand excluded by PLIP CD.23: 2 residues within 4Å: Chain B: H.107, D.110 Ligand excluded by PLIP CD.24: 1 residues within 4Å: Chain B: H.83 Ligand excluded by PLIP CD.25: 1 residues within 4Å: Chain B: H.83 Ligand excluded by PLIP CD.26: 1 residues within 4Å: Chain B: H.84 Ligand excluded by PLIP CD.27: 3 residues within 4Å: Chain C: H.45 Chain I: D.72, E.76 Ligand excluded by PLIP CD.28: 1 residues within 4Å: Chain C: H.57 Ligand excluded by PLIP CD.29: 1 residues within 4Å: Chain C: H.121 Ligand excluded by PLIP CD.30: 2 residues within 4Å: Chain C: E.114, E.117 Ligand excluded by PLIP CD.31: 2 residues within 4Å: Chain C: D.69, D.73 Ligand excluded by PLIP CD.32: 2 residues within 4Å: Chain C: E.25, H.29 Ligand excluded by PLIP CD.33: 2 residues within 4Å: Chain C: A.164 Chain J: H.107 Ligand excluded by PLIP CD.34: 3 residues within 4Å: Chain C: E.61, E.62, E.65 Ligand excluded by PLIP CD.35: 2 residues within 4Å: Chain C: E.125, E.128 Ligand excluded by PLIP CD.36: 2 residues within 4Å: Chain C: H.107, D.110 Ligand excluded by PLIP CD.37: 1 residues within 4Å: Chain C: H.83 Ligand excluded by PLIP CD.38: 1 residues within 4Å: Chain C: H.83 Ligand excluded by PLIP CD.39: 1 residues within 4Å: Chain C: H.84 Ligand excluded by PLIP CD.40: 3 residues within 4Å: Chain D: H.45 Chain G: D.72, E.76 Ligand excluded by PLIP CD.41: 1 residues within 4Å: Chain D: H.57 Ligand excluded by PLIP CD.42: 1 residues within 4Å: Chain D: H.121 Ligand excluded by PLIP CD.43: 2 residues within 4Å: Chain D: E.114, E.117 Ligand excluded by PLIP CD.44: 2 residues within 4Å: Chain D: D.69, D.73 Ligand excluded by PLIP CD.45: 2 residues within 4Å: Chain D: E.25, H.29 Ligand excluded by PLIP CD.46: 2 residues within 4Å: Chain B: H.107 Chain D: A.164 Ligand excluded by PLIP CD.47: 3 residues within 4Å: Chain D: E.61, E.62, E.65 Ligand excluded by PLIP CD.48: 2 residues within 4Å: Chain D: E.125, E.128 Ligand excluded by PLIP CD.49: 2 residues within 4Å: Chain D: H.107, D.110 Ligand excluded by PLIP CD.50: 1 residues within 4Å: Chain D: H.83 Ligand excluded by PLIP CD.51: 1 residues within 4Å: Chain D: H.83 Ligand excluded by PLIP CD.52: 1 residues within 4Å: Chain D: H.84 Ligand excluded by PLIP CD.53: 3 residues within 4Å: Chain B: D.72, E.76 Chain E: H.45 Ligand excluded by PLIP CD.54: 1 residues within 4Å: Chain E: H.57 Ligand excluded by PLIP CD.55: 1 residues within 4Å: Chain E: H.121 Ligand excluded by PLIP CD.56: 2 residues within 4Å: Chain E: E.114, E.117 Ligand excluded by PLIP CD.57: 2 residues within 4Å: Chain E: D.69, D.73 Ligand excluded by PLIP CD.58: 2 residues within 4Å: Chain E: E.25, H.29 Ligand excluded by PLIP CD.59: 2 residues within 4Å: Chain E: A.164 Chain L: H.107 Ligand excluded by PLIP CD.60: 3 residues within 4Å: Chain E: E.61, E.62, E.65 Ligand excluded by PLIP CD.61: 2 residues within 4Å: Chain E: E.125, E.128 Ligand excluded by PLIP CD.62: 2 residues within 4Å: Chain E: H.107, D.110 Ligand excluded by PLIP CD.63: 1 residues within 4Å: Chain E: H.83 Ligand excluded by PLIP CD.64: 1 residues within 4Å: Chain E: H.83 Ligand excluded by PLIP CD.65: 1 residues within 4Å: Chain E: H.84 Ligand excluded by PLIP CD.66: 3 residues within 4Å: Chain F: H.45 Chain L: D.72, E.76 Ligand excluded by PLIP CD.67: 1 residues within 4Å: Chain F: H.57 Ligand excluded by PLIP CD.68: 1 residues within 4Å: Chain F: H.121 Ligand excluded by PLIP CD.69: 2 residues within 4Å: Chain F: E.114, E.117 Ligand excluded by PLIP CD.70: 2 residues within 4Å: Chain F: D.69, D.73 Ligand excluded by PLIP CD.71: 2 residues within 4Å: Chain F: E.25, H.29 Ligand excluded by PLIP CD.72: 2 residues within 4Å: Chain F: A.164 Chain G: H.107 Ligand excluded by PLIP CD.73: 3 residues within 4Å: Chain F: E.61, E.62, E.65 Ligand excluded by PLIP CD.74: 2 residues within 4Å: Chain F: E.125, E.128 Ligand excluded by PLIP CD.75: 2 residues within 4Å: Chain F: H.107, D.110 Ligand excluded by PLIP CD.76: 1 residues within 4Å: Chain F: H.83 Ligand excluded by PLIP CD.77: 1 residues within 4Å: Chain F: H.83 Ligand excluded by PLIP CD.78: 1 residues within 4Å: Chain F: H.84 Ligand excluded by PLIP CD.79: 3 residues within 4Å: Chain D: D.72, E.76 Chain G: H.45 Ligand excluded by PLIP CD.80: 1 residues within 4Å: Chain G: H.57 Ligand excluded by PLIP CD.81: 1 residues within 4Å: Chain G: H.121 Ligand excluded by PLIP CD.82: 2 residues within 4Å: Chain G: E.114, E.117 Ligand excluded by PLIP CD.83: 2 residues within 4Å: Chain G: D.69, D.73 Ligand excluded by PLIP CD.84: 2 residues within 4Å: Chain G: E.25, H.29 Ligand excluded by PLIP CD.85: 2 residues within 4Å: Chain G: A.164 Chain K: H.107 Ligand excluded by PLIP CD.86: 3 residues within 4Å: Chain G: E.61, E.62, E.65 Ligand excluded by PLIP CD.87: 2 residues within 4Å: Chain G: E.125, E.128 Ligand excluded by PLIP CD.88: 2 residues within 4Å: Chain G: H.107, D.110 Ligand excluded by PLIP CD.89: 1 residues within 4Å: Chain G: H.83 Ligand excluded by PLIP CD.90: 1 residues within 4Å: Chain G: H.83 Ligand excluded by PLIP CD.91: 1 residues within 4Å: Chain G: H.84 Ligand excluded by PLIP CD.92: 3 residues within 4Å: Chain H: H.45 Chain K: D.72, E.76 Ligand excluded by PLIP CD.93: 1 residues within 4Å: Chain H: H.57 Ligand excluded by PLIP CD.94: 1 residues within 4Å: Chain H: H.121 Ligand excluded by PLIP CD.95: 2 residues within 4Å: Chain H: E.114, E.117 Ligand excluded by PLIP CD.96: 2 residues within 4Å: Chain H: D.69, D.73 Ligand excluded by PLIP CD.97: 2 residues within 4Å: Chain H: E.25, H.29 Ligand excluded by PLIP CD.98: 2 residues within 4Å: Chain C: H.107 Chain H: A.164 Ligand excluded by PLIP CD.99: 3 residues within 4Å: Chain H: E.61, E.62, E.65 Ligand excluded by PLIP CD.100: 2 residues within 4Å: Chain H: E.125, E.128 Ligand excluded by PLIP CD.101: 2 residues within 4Å: Chain H: H.107, D.110 Ligand excluded by PLIP CD.102: 1 residues within 4Å: Chain H: H.83 Ligand excluded by PLIP CD.103: 1 residues within 4Å: Chain H: H.83 Ligand excluded by PLIP CD.104: 1 residues within 4Å: Chain H: H.84 Ligand excluded by PLIP CD.105: 3 residues within 4Å: Chain C: D.72, E.76 Chain I: H.45 Ligand excluded by PLIP CD.106: 1 residues within 4Å: Chain I: H.57 Ligand excluded by PLIP CD.107: 1 residues within 4Å: Chain I: H.121 Ligand excluded by PLIP CD.108: 2 residues within 4Å: Chain I: E.114, E.117 Ligand excluded by PLIP CD.109: 2 residues within 4Å: Chain I: D.69, D.73 Ligand excluded by PLIP CD.110: 2 residues within 4Å: Chain I: E.25, H.29 Ligand excluded by PLIP CD.111: 2 residues within 4Å: Chain D: H.107 Chain I: A.164 Ligand excluded by PLIP CD.112: 3 residues within 4Å: Chain I: E.61, E.62, E.65 Ligand excluded by PLIP CD.113: 2 residues within 4Å: Chain I: E.125, E.128 Ligand excluded by PLIP CD.114: 2 residues within 4Å: Chain I: H.107, D.110 Ligand excluded by PLIP CD.115: 1 residues within 4Å: Chain I: H.83 Ligand excluded by PLIP CD.116: 1 residues within 4Å: Chain I: H.83 Ligand excluded by PLIP CD.117: 1 residues within 4Å: Chain I: H.84 Ligand excluded by PLIP CD.118: 3 residues within 4Å: Chain A: D.72, E.76 Chain J: H.45 Ligand excluded by PLIP CD.119: 1 residues within 4Å: Chain J: H.57 Ligand excluded by PLIP CD.120: 1 residues within 4Å: Chain J: H.121 Ligand excluded by PLIP CD.121: 2 residues within 4Å: Chain J: E.114, E.117 Ligand excluded by PLIP CD.122: 2 residues within 4Å: Chain J: D.69, D.73 Ligand excluded by PLIP CD.123: 2 residues within 4Å: Chain J: E.25, H.29 Ligand excluded by PLIP CD.124: 2 residues within 4Å: Chain H: H.107 Chain J: A.164 Ligand excluded by PLIP CD.125: 3 residues within 4Å: Chain J: E.61, E.62, E.65 Ligand excluded by PLIP CD.126: 2 residues within 4Å: Chain J: E.125, E.128 Ligand excluded by PLIP CD.127: 2 residues within 4Å: Chain J: H.107, D.110 Ligand excluded by PLIP CD.128: 1 residues within 4Å: Chain J: H.83 Ligand excluded by PLIP CD.129: 1 residues within 4Å: Chain J: H.83 Ligand excluded by PLIP CD.130: 1 residues within 4Å: Chain J: H.84 Ligand excluded by PLIP CD.131: 3 residues within 4Å: Chain H: D.72, E.76 Chain K: H.45 Ligand excluded by PLIP CD.132: 1 residues within 4Å: Chain K: H.57 Ligand excluded by PLIP CD.133: 1 residues within 4Å: Chain K: H.121 Ligand excluded by PLIP CD.134: 2 residues within 4Å: Chain K: E.114, E.117 Ligand excluded by PLIP CD.135: 2 residues within 4Å: Chain K: D.69, D.73 Ligand excluded by PLIP CD.136: 2 residues within 4Å: Chain K: E.25, H.29 Ligand excluded by PLIP CD.137: 2 residues within 4Å: Chain F: H.107 Chain K: A.164 Ligand excluded by PLIP CD.138: 3 residues within 4Å: Chain K: E.61, E.62, E.65 Ligand excluded by PLIP CD.139: 2 residues within 4Å: Chain K: E.125, E.128 Ligand excluded by PLIP CD.140: 2 residues within 4Å: Chain K: H.107, D.110 Ligand excluded by PLIP CD.141: 1 residues within 4Å: Chain K: H.83 Ligand excluded by PLIP CD.142: 1 residues within 4Å: Chain K: H.83 Ligand excluded by PLIP CD.143: 1 residues within 4Å: Chain K: H.84 Ligand excluded by PLIP CD.144: 3 residues within 4Å: Chain F: D.72, E.76 Chain L: H.45 Ligand excluded by PLIP CD.145: 1 residues within 4Å: Chain L: H.57 Ligand excluded by PLIP CD.146: 1 residues within 4Å: Chain L: H.121 Ligand excluded by PLIP CD.147: 2 residues within 4Å: Chain L: E.114, E.117 Ligand excluded by PLIP CD.148: 2 residues within 4Å: Chain L: D.69, D.73 Ligand excluded by PLIP CD.149: 2 residues within 4Å: Chain L: E.25, H.29 Ligand excluded by PLIP CD.150: 2 residues within 4Å: Chain A: H.107 Chain L: A.164 Ligand excluded by PLIP CD.151: 3 residues within 4Å: Chain L: E.61, E.62, E.65 Ligand excluded by PLIP CD.152: 2 residues within 4Å: Chain L: E.125, E.128 Ligand excluded by PLIP CD.153: 2 residues within 4Å: Chain L: H.107, D.110 Ligand excluded by PLIP CD.154: 1 residues within 4Å: Chain L: H.83 Ligand excluded by PLIP CD.155: 1 residues within 4Å: Chain L: H.83 Ligand excluded by PLIP CD.156: 1 residues within 4Å: Chain L: H.84 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yokoyama, H. et al., Crystal structure of Helicobacter pylori neutrophil-activating protein with a di-nuclear ferroxidase center in a zinc or cadmium-bound form. Biochem.Biophys.Res.Commun. (2012)

Release Date

2012-06-27

Peptides

Neutrophil-activating protein: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

G
A

H
A

I
A

J
A

K
A

L
A

Neutrophil-activating protein

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