SMTL ID : 7jgm.1 (1 other biounit)

Crystal Structure of the Ni-bound Human Heavy-chain variant 122H-delta C-star with meta-benzenedihyrdoxamate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.31 Å

Oligo State

homo-24-mer

Ligands

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

NI.1: 4 residues within 4Å: Chain A: E.27, E.62, H.65, Q.141 Ligand excluded by PLIP NI.2: 4 residues within 4Å: Chain A: H.173 Chain J: H.173 Chain M: H.173 Chain V: H.173 Ligand excluded by PLIP NI.4: 4 residues within 4Å: Chain B: E.27, E.62, H.65, Q.141 Ligand excluded by PLIP NI.5: 3 residues within 4Å: Chain A: H.122 Chain B: H.122 Chain C: H.122 Ligand excluded by PLIP NI.6: 4 residues within 4Å: Chain B: H.173 Chain E: H.173 Chain G: H.173 Chain L: H.173 Ligand excluded by PLIP NI.7: 4 residues within 4Å: Chain C: E.27, E.62, H.65, Q.141 Ligand excluded by PLIP NI.8: 4 residues within 4Å: Chain C: H.173 Chain D: H.173 Chain N: H.173 Chain Q: H.173 Ligand excluded by PLIP NI.9: 4 residues within 4Å: Chain D: E.27, E.62, H.65, Q.141 Ligand excluded by PLIP NI.10: 4 residues within 4Å: Chain D: H.122 Chain E: H.122 Chain F: H.122 Ligands: V9D.15 Ligand excluded by PLIP NI.12: 4 residues within 4Å: Chain E: E.27, E.62, H.65, Q.141 Ligand excluded by PLIP NI.13: 4 residues within 4Å: Chain F: E.27, E.62, H.65, Q.141 Ligand excluded by PLIP NI.14: 4 residues within 4Å: Chain F: H.173 Chain I: H.173 Chain R: H.173 Chain U: H.173 Ligand excluded by PLIP NI.16: 4 residues within 4Å: Chain G: E.27, E.62, H.65, Q.141 Ligand excluded by PLIP NI.17: 4 residues within 4Å: Chain G: H.122 Chain H: H.122 Chain I: H.122 Ligands: V9D.22 Ligand excluded by PLIP NI.19: 4 residues within 4Å: Chain H: E.27, E.62, H.65, Q.141 Ligand excluded by PLIP NI.20: 4 residues within 4Å: Chain H: H.173 Chain K: H.173 Chain S: H.173 Chain X: H.173 Ligand excluded by PLIP NI.21: 4 residues within 4Å: Chain I: E.27, E.62, H.65, Q.141 Ligand excluded by PLIP NI.23: 4 residues within 4Å: Chain J: E.27, E.62, H.65, Q.141 Ligand excluded by PLIP NI.25: 4 residues within 4Å: Chain K: E.27, E.62, H.65, Q.141 Ligand excluded by PLIP NI.26: 4 residues within 4Å: Chain L: E.27, E.62, H.65, Q.141 Ligand excluded by PLIP NI.27: 3 residues within 4Å: Chain J: H.122 Chain K: H.122 Chain L: H.122 Ligand excluded by PLIP NI.28: 4 residues within 4Å: Chain M: E.27, E.62, H.65, Q.141 Ligand excluded by PLIP NI.29: 3 residues within 4Å: Chain M: H.122 Chain N: H.122 Chain O: H.122 Ligand excluded by PLIP NI.31: 4 residues within 4Å: Chain N: E.27, E.62, H.65, Q.141 Ligand excluded by PLIP NI.32: 4 residues within 4Å: Chain O: E.27, E.62, H.65, Q.141 Ligand excluded by PLIP NI.33: 4 residues within 4Å: Chain O: H.173 Chain P: H.173 Chain T: H.173 Chain W: H.173 Ligand excluded by PLIP NI.34: 4 residues within 4Å: Chain P: E.27, E.62, H.65, Q.141 Ligand excluded by PLIP NI.35: 4 residues within 4Å: Chain P: H.122 Chain Q: H.122 Chain R: H.122 Ligands: V9D.39 Ligand excluded by PLIP NI.37: 4 residues within 4Å: Chain Q: E.27, E.62, H.65, Q.141 Ligand excluded by PLIP NI.38: 4 residues within 4Å: Chain R: E.27, E.62, H.65, Q.141 Ligand excluded by PLIP NI.40: 4 residues within 4Å: Chain S: E.27, E.62, H.65, Q.141 Ligand excluded by PLIP NI.41: 3 residues within 4Å: Chain S: H.122 Chain T: H.122 Chain U: H.122 Ligand excluded by PLIP NI.43: 4 residues within 4Å: Chain T: E.27, E.62, H.65, Q.141 Ligand excluded by PLIP NI.44: 4 residues within 4Å: Chain U: E.27, E.62, H.65, Q.141 Ligand excluded by PLIP NI.45: 4 residues within 4Å: Chain V: E.27, E.62, H.65, Q.141 Ligand excluded by PLIP NI.47: 4 residues within 4Å: Chain W: E.27, E.62, H.65, Q.141 Ligand excluded by PLIP NI.49: 4 residues within 4Å: Chain X: E.27, E.62, H.65, Q.141 Ligand excluded by PLIP NI.50: 4 residues within 4Å: Chain V: H.122 Chain W: H.122 Chain X: H.122 Ligands: V9D.48 Ligand excluded by PLIP

8 x NA: SODIUM ION(Non-functional Binders)

NA.3: 6 residues within 4Å: Chain A: D.131, E.134 Chain B: D.131, E.134 Chain C: D.131, E.134 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:D.131, B:D.131 NA.11: 6 residues within 4Å: Chain D: D.131, E.134 Chain E: D.131, E.134 Chain F: D.131, E.134 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain F Hydrogen bonds: D:D.131, D:D.131, D:E.134, F:D.131 NA.18: 6 residues within 4Å: Chain G: D.131, E.134 Chain H: D.131, E.134 Chain I: D.131, E.134 5 PLIP interactions: 2 interactions with chain H, 2 interactions with chain G, 1 interactions with chain I Hydrogen bonds: H:D.131, G:D.131, I:D.131 Water bridges: H:T.135, G:T.135 NA.24: 6 residues within 4Å: Chain J: D.131, E.134 Chain K: D.131, E.134 Chain L: D.131, E.134 2 PLIP interactions: 2 interactions with chain L Hydrogen bonds: L:D.131, L:D.131 NA.30: 6 residues within 4Å: Chain M: D.131, E.134 Chain N: D.131, E.134 Chain O: D.131, E.134 4 PLIP interactions: 2 interactions with chain O, 2 interactions with chain M Hydrogen bonds: O:D.131, O:E.134, M:E.134, M:E.134 NA.36: 6 residues within 4Å: Chain P: D.131, E.134 Chain Q: D.131, E.134 Chain R: D.131, E.134 4 PLIP interactions: 1 interactions with chain Q, 2 interactions with chain P, 1 interactions with chain R Hydrogen bonds: Q:D.131, P:D.131, P:E.134, R:D.131 NA.42: 6 residues within 4Å: Chain S: D.131, E.134 Chain T: D.131, E.134 Chain U: D.131, E.134 5 PLIP interactions: 3 interactions with chain S, 2 interactions with chain U Hydrogen bonds: S:D.131, S:E.134, U:D.131 Water bridges: S:T.135, U:T.135 NA.46: 6 residues within 4Å: Chain V: D.131, E.134 Chain W: D.131, E.134 Chain X: D.131, E.134 2 PLIP interactions: 1 interactions with chain V, 1 interactions with chain X Hydrogen bonds: V:E.134, X:D.131

4 x V9D: N~1~,N~3~-dihydroxybenzene-1,3-dicarboxamide(Non-covalent)

V9D.15: 6 residues within 4Å: Chain D: H.122 Chain E: H.122 Chain F: K.119, H.122, D.123 Ligands: NI.10 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:H.122 V9D.22: 6 residues within 4Å: Chain G: H.122 Chain H: H.122 Chain I: K.119, H.122, D.123 Ligands: NI.17 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:H.122 V9D.39: 5 residues within 4Å: Chain P: H.122 Chain Q: H.122, D.123 Chain R: H.122 Ligands: NI.35 1 PLIP interactions: 1 interactions with chain R Hydrogen bonds: R:H.122 V9D.48: 5 residues within 4Å: Chain V: H.122 Chain W: H.122, D.123 Chain X: H.122 Ligands: NI.50 1 PLIP interactions: 1 interactions with chain X Hydrogen bonds: X:H.122

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bailey, J.B. et al., Tunable and Cooperative Thermomechanical Properties of Protein-Metal-Organic Frameworks. J.Am.Chem.Soc. (2020)

Release Date

2020-10-14

Peptides

Ferritin heavy chain: ABCDEFGHIJKLMNOPQRSTUVWX

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

M
M

N
N

O
O

P
P

Q
Q

R
R

S
S

T
T

U
U

V
V

W
W

X
X

Ferritin heavy chain

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