SMTL ID : 5vxx.1

Cryo-EM reconstruction of Neisseria gonorrhoeae Type IV pilus

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 5.10 Å

Oligo State

homo-21-mer

Ligands

21 x B6D- GLA: alpha-D-galactopyranose-(1-3)-2,4-bisacetamido-2,4,6-trideoxy-beta-D-glucopyranose(Post Translational Modification)

B6D-GLA.1: 6 residues within 4Å: Chain A: Y.50, K.56, E.59, N.60, T.62, S.63 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.50, A:K.56 Hydrogen bonds: A:N.60, A:T.62 B6D-GLA.2: 6 residues within 4Å: Chain B: Y.50, K.56, E.59, N.60, T.62, S.63 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.50, B:K.56 Hydrogen bonds: B:N.60, B:T.62 B6D-GLA.3: 6 residues within 4Å: Chain C: Y.50, K.56, E.59, N.60, T.62, S.63 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:Y.50, C:K.56 Hydrogen bonds: C:N.60, C:T.62 B6D-GLA.4: 6 residues within 4Å: Chain D: Y.50, K.56, E.59, N.60, T.62, S.63 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:Y.50, D:K.56 Hydrogen bonds: D:N.60, D:T.62 B6D-GLA.5: 6 residues within 4Å: Chain E: Y.50, K.56, E.59, N.60, T.62, S.63 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:Y.50, E:K.56 Hydrogen bonds: E:N.60, E:T.62 B6D-GLA.6: 6 residues within 4Å: Chain F: Y.50, K.56, E.59, N.60, T.62, S.63 4 PLIP interactions: 4 interactions with chain F Hydrophobic interactions: F:Y.50, F:K.56 Hydrogen bonds: F:N.60, F:T.62 B6D-GLA.7: 6 residues within 4Å: Chain G: Y.50, K.56, E.59, N.60, T.62, S.63 4 PLIP interactions: 4 interactions with chain G Hydrophobic interactions: G:Y.50, G:K.56 Hydrogen bonds: G:N.60, G:T.62 B6D-GLA.8: 6 residues within 4Å: Chain H: Y.50, K.56, E.59, N.60, T.62, S.63 4 PLIP interactions: 4 interactions with chain H Hydrophobic interactions: H:Y.50, H:K.56 Hydrogen bonds: H:N.60, H:T.62 B6D-GLA.9: 6 residues within 4Å: Chain I: Y.50, K.56, E.59, N.60, T.62, S.63 4 PLIP interactions: 4 interactions with chain I Hydrophobic interactions: I:Y.50, I:K.56 Hydrogen bonds: I:N.60, I:T.62 B6D-GLA.10: 6 residues within 4Å: Chain J: Y.50, K.56, E.59, N.60, T.62, S.63 4 PLIP interactions: 4 interactions with chain J Hydrophobic interactions: J:Y.50, J:K.56 Hydrogen bonds: J:N.60, J:T.62 B6D-GLA.11: 6 residues within 4Å: Chain K: Y.50, K.56, E.59, N.60, T.62, S.63 4 PLIP interactions: 4 interactions with chain K Hydrophobic interactions: K:Y.50, K:K.56 Hydrogen bonds: K:N.60, K:T.62 B6D-GLA.12: 6 residues within 4Å: Chain L: Y.50, K.56, E.59, N.60, T.62, S.63 4 PLIP interactions: 4 interactions with chain L Hydrophobic interactions: L:Y.50, L:K.56 Hydrogen bonds: L:N.60, L:T.62 B6D-GLA.13: 6 residues within 4Å: Chain M: Y.50, K.56, E.59, N.60, T.62, S.63 4 PLIP interactions: 4 interactions with chain M Hydrophobic interactions: M:Y.50, M:K.56 Hydrogen bonds: M:N.60, M:T.62 B6D-GLA.14: 6 residues within 4Å: Chain N: Y.50, K.56, E.59, N.60, T.62, S.63 4 PLIP interactions: 4 interactions with chain N Hydrophobic interactions: N:Y.50, N:K.56 Hydrogen bonds: N:N.60, N:T.62 B6D-GLA.15: 6 residues within 4Å: Chain O: Y.50, K.56, E.59, N.60, T.62, S.63 4 PLIP interactions: 4 interactions with chain O Hydrophobic interactions: O:Y.50, O:K.56 Hydrogen bonds: O:N.60, O:T.62 B6D-GLA.16: 6 residues within 4Å: Chain P: Y.50, K.56, E.59, N.60, T.62, S.63 4 PLIP interactions: 4 interactions with chain P Hydrophobic interactions: P:Y.50, P:K.56 Hydrogen bonds: P:N.60, P:T.62 B6D-GLA.17: 6 residues within 4Å: Chain Q: Y.50, K.56, E.59, N.60, T.62, S.63 4 PLIP interactions: 4 interactions with chain Q Hydrophobic interactions: Q:Y.50, Q:K.56 Hydrogen bonds: Q:N.60, Q:T.62 B6D-GLA.18: 6 residues within 4Å: Chain R: Y.50, K.56, E.59, N.60, T.62, S.63 4 PLIP interactions: 4 interactions with chain R Hydrophobic interactions: R:Y.50, R:K.56 Hydrogen bonds: R:N.60, R:T.62 B6D-GLA.19: 6 residues within 4Å: Chain S: Y.50, K.56, E.59, N.60, T.62, S.63 4 PLIP interactions: 4 interactions with chain S Hydrophobic interactions: S:Y.50, S:K.56 Hydrogen bonds: S:N.60, S:T.62 B6D-GLA.20: 6 residues within 4Å: Chain T: Y.50, K.56, E.59, N.60, T.62, S.63 4 PLIP interactions: 4 interactions with chain T Hydrophobic interactions: T:Y.50, T:K.56 Hydrogen bonds: T:N.60, T:T.62 B6D-GLA.21: 6 residues within 4Å: Chain U: Y.50, K.56, E.59, N.60, T.62, S.63 4 PLIP interactions: 4 interactions with chain U Hydrophobic interactions: U:Y.50, U:K.56 Hydrogen bonds: U:N.60, U:T.62

21 x OPE: PHOSPHORIC ACID MONO-(2-AMINO-ETHYL) ESTER(Covalent)

OPE.22: 2 residues within 4Å: Chain A: S.68, S.69 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.68, A:S.69 OPE.23: 2 residues within 4Å: Chain B: S.68, S.69 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.68, B:S.69 OPE.24: 2 residues within 4Å: Chain C: S.68, S.69 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.68, C:S.69 OPE.25: 2 residues within 4Å: Chain D: S.68, S.69 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:S.68, D:S.69 OPE.26: 2 residues within 4Å: Chain E: S.68, S.69 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:S.68, E:S.69 OPE.27: 2 residues within 4Å: Chain F: S.68, S.69 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:S.68, F:S.69 OPE.28: 2 residues within 4Å: Chain G: S.68, S.69 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:S.68, G:S.69 OPE.29: 2 residues within 4Å: Chain H: S.68, S.69 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:S.68, H:S.69 OPE.30: 2 residues within 4Å: Chain I: S.68, S.69 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:S.68, I:S.69 OPE.31: 2 residues within 4Å: Chain J: S.68, S.69 2 PLIP interactions: 2 interactions with chain J Hydrogen bonds: J:S.68, J:S.69 OPE.32: 2 residues within 4Å: Chain K: S.68, S.69 2 PLIP interactions: 2 interactions with chain K Hydrogen bonds: K:S.68, K:S.69 OPE.33: 2 residues within 4Å: Chain L: S.68, S.69 2 PLIP interactions: 2 interactions with chain L Hydrogen bonds: L:S.68, L:S.69 OPE.34: 2 residues within 4Å: Chain M: S.68, S.69 2 PLIP interactions: 2 interactions with chain M Hydrogen bonds: M:S.68, M:S.69 OPE.35: 2 residues within 4Å: Chain N: S.68, S.69 2 PLIP interactions: 2 interactions with chain N Hydrogen bonds: N:S.68, N:S.69 OPE.36: 2 residues within 4Å: Chain O: S.68, S.69 2 PLIP interactions: 2 interactions with chain O Hydrogen bonds: O:S.68, O:S.69 OPE.37: 2 residues within 4Å: Chain P: S.68, S.69 2 PLIP interactions: 2 interactions with chain P Hydrogen bonds: P:S.68, P:S.69 OPE.38: 2 residues within 4Å: Chain Q: S.68, S.69 2 PLIP interactions: 2 interactions with chain Q Hydrogen bonds: Q:S.68, Q:S.69 OPE.39: 2 residues within 4Å: Chain R: S.68, S.69 2 PLIP interactions: 2 interactions with chain R Hydrogen bonds: R:S.68, R:S.69 OPE.40: 2 residues within 4Å: Chain S: S.68, S.69 2 PLIP interactions: 2 interactions with chain S Hydrogen bonds: S:S.68, S:S.69 OPE.41: 2 residues within 4Å: Chain T: S.68, S.69 2 PLIP interactions: 2 interactions with chain T Hydrogen bonds: T:S.68, T:S.69 OPE.42: 2 residues within 4Å: Chain U: S.68, S.69 2 PLIP interactions: 2 interactions with chain U Hydrogen bonds: U:S.68, U:S.69

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, F. et al., Cryoelectron Microscopy Reconstructions of the Pseudomonas aeruginosa and Neisseria gonorrhoeae Type IV Pili at Sub-nanometer Resolution. Structure (2017)

Release Date

2017-07-12

Peptides

Fimbrial protein: ABCDEFGHIJKLMNOPQRSTU

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

Membrane

We predict this structure to be a membrane protein.
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Fimbrial protein

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