SMTL ID : 7d74.1

Cryo-EM structure of GMPPA/GMPPB complex bound to GTP (state II)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-8-mer

Ligands

12 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)(Covalent)

GTP.1: 21 residues within 4Å: Chain A: L.7, I.8, G.9, K.13, I.56, G.57, F.58, E.85, L.89, G.90, T.91, N.114, A.115, D.116, Y.167, E.169, N.180, Y.184, E.223, Q.247, K.249 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:I.56, A:L.89, A:G.90, A:N.114, A:A.115, A:D.116, A:D.116, A:N.180, A:N.180, A:Y.184, A:Q.247 Salt bridges: A:E.85, A:K.249, A:K.249 GTP.2: 21 residues within 4Å: Chain B: L.7, I.8, G.9, K.13, I.56, G.57, F.58, E.85, L.89, G.90, T.91, N.114, A.115, D.116, Y.167, E.169, N.180, Y.184, E.223, Q.247, K.249 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:I.56, B:L.89, B:G.90, B:N.114, B:A.115, B:D.116, B:D.116, B:Y.167, B:N.180, B:N.180, B:Y.184, B:Y.184, B:E.223, B:Q.247 Salt bridges: B:E.85, B:K.249, B:K.249 GTP.3: 21 residues within 4Å: Chain C: L.7, I.8, G.9, K.13, I.56, G.57, F.58, E.85, L.89, G.90, T.91, N.114, A.115, D.116, Y.167, E.169, N.180, Y.184, E.223, Q.247, K.249 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:I.56, C:L.89, C:G.90, C:N.114, C:A.115, C:D.116, C:D.116, C:Y.167, C:N.180, C:N.180, C:Y.184, C:E.223, C:Q.247 Salt bridges: C:E.85, C:K.249, C:K.249 GTP.4: 21 residues within 4Å: Chain D: L.7, I.8, G.9, K.13, I.56, G.57, F.58, E.85, L.89, G.90, T.91, N.114, A.115, D.116, Y.167, E.169, N.180, Y.184, E.223, Q.247, K.249 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:I.56, D:L.89, D:G.90, D:N.114, D:A.115, D:D.116, D:D.116, D:N.180, D:N.180, D:Y.184, D:Y.184, D:Q.247 Salt bridges: D:E.85, D:K.249, D:K.249 GTP.5: 18 residues within 4Å: Chain E: L.6, V.7, G.8, G.9, G.11, T.12, R.13, K.23, A.52, V.53, S.54, P.83, L.84, G.85, T.86, N.108, S.109, D.110 17 PLIP interactions: 17 interactions with chain E Hydrogen bonds: E:G.9, E:G.9, E:G.11, E:T.12, E:R.13, E:A.52, E:S.54, E:S.54, E:S.54, E:L.84, E:G.85, E:S.109, E:D.110 Salt bridges: E:K.23, E:K.23, E:K.23, E:E.80 GTP.6: 18 residues within 4Å: Chain F: L.6, V.7, G.8, G.9, Y.10, G.11, T.12, R.13, K.23, A.52, V.53, S.54, E.80, P.83, L.84, G.85, S.109, D.110 15 PLIP interactions: 15 interactions with chain F Hydrogen bonds: F:G.8, F:G.9, F:G.9, F:T.12, F:R.13, F:V.53, F:S.54, F:S.54, F:S.54, F:L.84, F:G.85 Salt bridges: F:K.23, F:K.23, F:K.23, F:E.80 GTP.7: 18 residues within 4Å: Chain G: L.6, G.8, G.9, G.11, T.12, R.13, K.23, A.52, V.53, S.54, E.80, P.83, L.84, G.85, T.86, N.108, S.109, D.110 17 PLIP interactions: 17 interactions with chain G Hydrogen bonds: G:G.8, G:G.8, G:G.9, G:G.9, G:T.12, G:R.13, G:S.54, G:S.54, G:S.54, G:L.84, G:G.85, G:S.109 Salt bridges: G:R.13, G:K.23, G:K.23, G:K.23, G:E.80 GTP.8: 19 residues within 4Å: Chain H: L.6, V.7, G.8, G.9, G.11, T.12, R.13, K.23, A.52, V.53, S.54, E.80, P.83, L.84, G.85, T.86, N.108, S.109, D.110 16 PLIP interactions: 16 interactions with chain H Hydrogen bonds: H:G.8, H:G.9, H:G.9, H:T.12, H:R.13, H:V.53, H:S.54, H:S.54, H:L.84, H:G.85, H:S.109 Salt bridges: H:R.13, H:K.23, H:K.23, H:K.23, H:E.80 GTP.9: 19 residues within 4Å: Chain I: L.6, V.7, G.8, G.9, Y.10, G.11, T.12, R.13, K.23, A.52, V.53, S.54, E.80, P.83, L.84, G.85, N.108, S.109, D.110 16 PLIP interactions: 16 interactions with chain I Hydrogen bonds: I:V.7, I:G.8, I:G.9, I:T.12, I:R.13, I:S.54, I:S.54, I:L.84, I:G.85, I:N.108, I:S.109 Salt bridges: I:R.13, I:K.23, I:K.23, I:K.23, I:E.80 GTP.10: 19 residues within 4Å: Chain J: L.6, V.7, G.8, G.9, Y.10, G.11, T.12, R.13, K.23, A.52, V.53, S.54, E.80, P.83, L.84, G.85, N.108, S.109, D.110 18 PLIP interactions: 18 interactions with chain J Hydrogen bonds: J:G.8, J:G.9, J:G.9, J:G.9, J:T.12, J:R.13, J:A.52, J:S.54, J:S.54, J:S.54, J:L.84, J:G.85, J:S.109 Salt bridges: J:R.13, J:K.23, J:K.23, J:K.23, J:E.80 GTP.11: 18 residues within 4Å: Chain K: L.6, V.7, G.8, G.9, G.11, T.12, R.13, K.23, A.52, V.53, S.54, E.80, P.83, L.84, G.85, N.108, S.109, D.110 16 PLIP interactions: 16 interactions with chain K Hydrogen bonds: K:G.8, K:G.9, K:G.9, K:T.12, K:R.13, K:A.52, K:S.54, K:S.54, K:L.84, K:G.85, K:S.109 Salt bridges: K:R.13, K:K.23, K:K.23, K:K.23, K:E.80 GTP.12: 19 residues within 4Å: Chain L: L.6, V.7, G.8, G.9, Y.10, G.11, T.12, R.13, K.23, A.52, V.53, S.54, P.83, L.84, G.85, T.86, N.108, S.109, D.110 15 PLIP interactions: 15 interactions with chain L Hydrogen bonds: L:V.7, L:G.8, L:G.9, L:R.13, L:R.13, L:S.54, L:S.54, L:S.54, L:L.84, L:G.85, L:S.109 Salt bridges: L:R.13, L:K.23, L:K.23, L:K.23

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zheng, L. et al., Cryo-EM structures of human GMPPA-GMPPB complex reveal how cells maintain GDP-mannose homeostasis. Nat.Struct.Mol.Biol. (2021)

Release Date

2021-05-19

Peptides

Mannose-1-phosphate guanyltransferase alpha: ABCD
Mannose-1-phosphate guanyltransferase beta: EFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

C
B

D
C

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

Mannose-1-phosphate guanyltransferase alpha

Mannose-1-phosphate guanyltransferase beta

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