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

human GCH-GFRP inhibitory complex 7-deaza-GTP bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.21 Å

Oligo State

hetero-10-10-mer

Ligands

10 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.100, H.103, C.171 Ligands: QBQ.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.100, A:H.103, A:C.171 ZN.5: 5 residues within 4Å: Chain B: C.100, H.102, H.103, C.171 Ligands: QBQ.9 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.100, B:H.103, B:C.171 ZN.8: 4 residues within 4Å: Chain C: C.100, H.103, C.171 Ligands: QBQ.11 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.100, C:H.103, C:C.171 ZN.10: 4 residues within 4Å: Chain D: C.100, H.103, C.171 Ligands: QBQ.14 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.100, D:H.103, D:C.171 ZN.13: 4 residues within 4Å: Chain E: C.100, H.103, C.171 Ligands: QBQ.2 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:C.100, E:H.103, E:C.171 ZN.16: 4 residues within 4Å: Chain F: C.100, H.103, C.171 Ligands: QBQ.20 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:C.100, F:H.103, F:C.171 ZN.19: 4 residues within 4Å: Chain G: C.100, H.103, C.171 Ligands: QBQ.23 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:C.100, G:H.103, G:C.171 ZN.22: 4 residues within 4Å: Chain H: C.100, H.103, C.171 Ligands: QBQ.26 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:C.100, H:H.103, H:C.171 ZN.25: 4 residues within 4Å: Chain I: C.100, H.103, C.171 Ligands: QBQ.30 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:C.100, I:H.103, I:C.171 ZN.29: 4 residues within 4Å: Chain J: C.100, H.103, C.171 Ligands: QBQ.17 3 PLIP interactions: 3 interactions with chain J Metal complexes: J:C.100, J:H.103, J:C.171

10 x QBQ: 7-deaza-GTP(Non-covalent)

QBQ.2: 22 residues within 4Å: Chain A: N.77, A.79, F.81, V.121, L.122, G.123, L.124, S.125, K.126, R.129 Chain E: C.100, H.102, H.103, V.140, Q.141, E.142, H.169, C.171, R.175, G.176 Chain F: R.56 Ligands: ZN.13 24 PLIP interactions: 13 interactions with chain A, 1 interactions with chain F, 10 interactions with chain E Hydrophobic interactions: A:L.124 Hydrogen bonds: A:N.77, A:L.122, A:L.124, A:S.125, A:S.125, A:S.125, A:K.126, E:Q.141 Water bridges: A:R.129, E:H.103, E:R.175, E:R.175 Salt bridges: A:K.126, A:K.126, A:K.126, A:R.129, F:R.56, E:H.103, E:H.103, E:E.142, E:R.175, E:R.175 pi-Cation interactions: E:H.102 QBQ.6: 20 residues within 4Å: Chain A: C.100, H.102, H.103, V.140, Q.141, E.142, H.169, R.175 Chain B: N.77, A.79, F.81, V.121, L.122, G.123, L.124, S.125, K.126, R.129 Chain J: R.56 Ligands: ZN.1 23 PLIP interactions: 11 interactions with chain A, 11 interactions with chain B, 1 interactions with chain J Hydrogen bonds: A:Q.141, B:N.77, B:L.122, B:L.124, B:S.125, B:S.125, B:K.126 Water bridges: A:H.103, A:R.175, A:R.175, A:R.175, B:L.122 Salt bridges: A:H.103, A:H.103, A:E.142, A:R.175, A:R.175, B:K.126, B:K.126, B:K.126, B:R.129, J:R.56 pi-Cation interactions: A:H.102 QBQ.9: 23 residues within 4Å: Chain B: C.100, H.102, H.103, V.140, Q.141, E.142, H.169, C.171, R.175, G.176 Chain C: N.77, A.79, F.81, V.121, L.122, G.123, L.124, S.125, K.126, R.129 Chain I: K.52, R.56 Ligands: ZN.5 22 PLIP interactions: 8 interactions with chain B, 13 interactions with chain C, 1 interactions with chain I Hydrogen bonds: B:Q.141, C:N.77, C:L.122, C:L.124, C:S.125, C:S.125, C:S.125, C:K.126 Water bridges: B:R.175, B:R.175, C:R.129 Salt bridges: B:H.103, B:E.142, B:R.175, B:R.175, C:K.126, C:K.126, C:K.126, C:R.129, I:R.56 pi-Stacking: B:H.102 Hydrophobic interactions: C:L.124 QBQ.11: 23 residues within 4Å: Chain C: C.100, H.102, H.103, V.140, Q.141, E.142, H.169, C.171, R.175, G.176 Chain D: N.77, A.79, F.81, V.121, L.122, G.123, L.124, S.125, K.126, R.129 Chain H: K.52, R.56 Ligands: ZN.8 26 PLIP interactions: 14 interactions with chain D, 11 interactions with chain C, 1 interactions with chain H Hydrophobic interactions: D:L.124 Hydrogen bonds: D:N.77, D:L.122, D:L.124, D:S.125, D:S.125, D:K.126, D:K.126, D:K.126, C:Q.141 Water bridges: D:R.129, C:H.103, C:R.175, C:R.175, C:V.177 Salt bridges: D:K.126, D:K.126, D:K.126, D:R.129, C:H.103, C:H.103, C:E.142, C:R.175, C:R.175, H:R.56 pi-Cation interactions: C:H.102 QBQ.14: 21 residues within 4Å: Chain D: C.100, H.102, H.103, V.140, Q.141, E.142, H.169, C.171, R.175, G.176 Chain E: N.77, A.79, V.121, L.122, G.123, L.124, S.125, K.126, R.129 Chain G: R.56 Ligands: ZN.10 25 PLIP interactions: 10 interactions with chain D, 13 interactions with chain E, 2 interactions with chain G Hydrogen bonds: D:Q.141, E:N.77, E:L.122, E:L.124, E:S.125, E:S.125, E:K.126, E:K.126, E:K.126 Water bridges: D:H.103, D:R.175, D:V.177, D:V.177, G:S.59 Salt bridges: D:H.103, D:E.142, D:R.175, D:R.175, E:K.126, E:K.126, E:K.126, E:R.129, G:R.56 pi-Stacking: D:H.102 Hydrophobic interactions: E:L.124 QBQ.17: 22 residues within 4Å: Chain A: R.56 Chain F: N.77, A.79, F.81, V.121, L.122, G.123, L.124, S.125, K.126, R.129 Chain J: C.100, H.102, H.103, V.140, Q.141, E.142, H.169, C.171, R.175, G.176 Ligands: ZN.29 27 PLIP interactions: 11 interactions with chain J, 14 interactions with chain F, 2 interactions with chain A Hydrogen bonds: J:Q.141, F:N.77, F:L.122, F:L.124, F:S.125, F:S.125, F:S.125, F:K.126 Water bridges: J:R.175, J:R.175, J:R.175, J:R.175, F:R.129, F:R.129, A:K.52 Salt bridges: J:H.103, J:H.103, J:E.142, J:R.175, J:R.175, F:K.126, F:K.126, F:K.126, F:R.129, A:R.56 pi-Stacking: J:H.102 Hydrophobic interactions: F:L.124 QBQ.20: 23 residues within 4Å: Chain E: K.52, R.56 Chain F: C.100, H.102, H.103, V.140, Q.141, E.142, H.169, C.171, R.175, G.176 Chain G: N.77, A.79, F.81, V.121, L.122, G.123, L.124, S.125, K.126, R.129 Ligands: ZN.16 27 PLIP interactions: 14 interactions with chain G, 11 interactions with chain F, 2 interactions with chain E Hydrophobic interactions: G:L.124 Hydrogen bonds: G:N.77, G:N.77, G:L.122, G:L.124, G:S.125, G:S.125, G:S.125, G:K.126, F:Q.141 Water bridges: G:L.122, F:R.175, F:R.175, F:R.175, F:R.175 Salt bridges: G:K.126, G:K.126, G:K.126, G:R.129, F:H.103, F:H.103, F:E.142, F:R.175, F:R.175, E:K.52, E:R.56 pi-Cation interactions: F:H.102 QBQ.23: 22 residues within 4Å: Chain D: R.56 Chain G: C.100, H.102, H.103, V.140, Q.141, E.142, H.169, C.171, R.175, G.176 Chain H: N.77, A.79, F.81, V.121, L.122, G.123, L.124, S.125, K.126, R.129 Ligands: ZN.19 23 PLIP interactions: 12 interactions with chain H, 10 interactions with chain G, 1 interactions with chain D Hydrophobic interactions: H:L.124 Hydrogen bonds: H:N.77, H:L.122, H:L.124, H:S.125, H:S.125, H:S.125, H:K.126, G:Q.141 Salt bridges: H:K.126, H:K.126, H:K.126, H:R.129, G:H.103, G:H.103, G:E.142, G:R.175, G:R.175, D:R.56 Water bridges: G:R.175, G:R.175, G:R.175 pi-Cation interactions: G:H.102 QBQ.26: 22 residues within 4Å: Chain C: R.56 Chain H: C.100, H.102, H.103, V.140, Q.141, E.142, H.169, C.171, R.175, G.176 Chain I: N.77, A.79, F.81, V.121, L.122, G.123, L.124, S.125, K.126, R.129 Ligands: ZN.22 25 PLIP interactions: 13 interactions with chain I, 11 interactions with chain H, 1 interactions with chain C Hydrophobic interactions: I:L.124 Hydrogen bonds: I:N.77, I:L.122, I:L.124, I:S.125, I:S.125, I:S.125, I:K.126, H:Q.141 Water bridges: I:K.126, H:H.103, H:R.175, H:R.175, H:R.175 Salt bridges: I:K.126, I:K.126, I:K.126, I:R.129, H:H.103, H:H.103, H:E.142, H:R.175, H:R.175, C:R.56 pi-Stacking: H:H.102 QBQ.30: 22 residues within 4Å: Chain B: R.56 Chain I: C.100, H.102, H.103, V.140, Q.141, E.142, H.169, C.171, R.175, G.176 Chain J: N.77, A.79, F.81, V.121, L.122, G.123, L.124, S.125, K.126, R.129 Ligands: ZN.25 23 PLIP interactions: 10 interactions with chain I, 12 interactions with chain J, 1 interactions with chain B Hydrogen bonds: I:Q.141, J:N.77, J:L.122, J:L.124, J:S.125, J:S.125, J:S.125, J:K.126 Water bridges: I:R.175, I:R.175, I:V.177, J:L.122 Salt bridges: I:H.103, I:H.103, I:E.142, I:R.175, I:R.175, J:K.126, J:K.126, J:K.126, J:R.129, B:R.56 pi-Cation interactions: I:H.102

10 x HBI: 7,8-DIHYDROBIOPTERIN(Non-covalent)

HBI.3: 13 residues within 4Å: Chain A: D.86, E.87, M.88, L.116, A.159, V.192, T.199, E.202 Chain E: S.187, T.188, M.189, R.194, R.200 14 PLIP interactions: 6 interactions with chain E, 8 interactions with chain A Hydrogen bonds: E:S.187, E:R.200, E:R.200, A:D.86, A:M.88 Water bridges: E:R.194, E:R.194, A:T.199, A:T.199 pi-Cation interactions: E:R.194 Hydrophobic interactions: A:L.116, A:A.159, A:V.192 Salt bridges: A:E.202 HBI.4: 13 residues within 4Å: Chain A: S.187, T.188, M.189, R.194, R.200 Chain B: D.86, E.87, M.88, L.116, A.159, V.192, T.199, E.202 12 PLIP interactions: 6 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:S.187, A:R.200, A:R.200, B:D.86, B:M.88 Water bridges: A:M.189, A:M.189 pi-Cation interactions: A:R.194 Hydrophobic interactions: B:L.116, B:A.159, B:V.192 Salt bridges: B:E.202 HBI.7: 13 residues within 4Å: Chain B: S.187, T.188, M.189, R.194, R.200 Chain C: D.86, E.87, M.88, L.116, A.159, V.192, T.199, E.202 12 PLIP interactions: 6 interactions with chain C, 6 interactions with chain B Hydrophobic interactions: C:L.116, C:A.159, C:V.192 Hydrogen bonds: C:D.86, C:M.88, B:S.187, B:R.200, B:R.200 Salt bridges: C:E.202 Water bridges: B:M.189, B:R.194 pi-Cation interactions: B:R.194 HBI.12: 13 residues within 4Å: Chain C: S.187, T.188, M.189, R.194, R.200 Chain D: D.86, E.87, M.88, L.116, A.159, V.192, T.199, E.202 13 PLIP interactions: 8 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:A.159, D:V.192 Hydrogen bonds: D:D.86, D:M.88, C:S.187, C:R.200, C:R.200 Water bridges: D:D.86, D:T.199, D:T.199, C:M.189, C:M.189 Salt bridges: D:E.202 HBI.15: 13 residues within 4Å: Chain D: S.187, T.188, M.189, R.194, R.200 Chain E: D.86, E.87, M.88, L.116, A.159, V.192, T.199, E.202 17 PLIP interactions: 10 interactions with chain E, 2 interactions with chain N, 5 interactions with chain D Hydrophobic interactions: E:L.116, E:A.159, E:V.192 Hydrogen bonds: E:D.86, E:M.88, D:S.187, D:R.200, D:R.200 Water bridges: E:D.86, E:D.196, E:T.199, E:T.199, N:Q.12, N:Q.12, D:M.189, D:R.194 Salt bridges: E:E.202 HBI.18: 13 residues within 4Å: Chain F: D.86, E.87, M.88, L.116, A.159, V.192, T.199, E.202 Chain J: S.187, T.188, M.189, R.194, R.200 14 PLIP interactions: 7 interactions with chain J, 7 interactions with chain F Hydrogen bonds: J:S.187, J:M.189, J:R.200, J:R.200, F:D.86, F:M.88 Water bridges: J:R.194, J:R.194, F:T.199, F:T.199 pi-Cation interactions: J:R.194 Hydrophobic interactions: F:A.159, F:V.192 Salt bridges: F:E.202 HBI.21: 13 residues within 4Å: Chain F: S.187, T.188, M.189, R.194, R.200 Chain G: D.86, E.87, M.88, L.116, A.159, V.192, T.199, E.202 14 PLIP interactions: 6 interactions with chain F, 8 interactions with chain G Hydrogen bonds: F:S.187, F:R.200, F:R.200, G:D.86, G:M.88 Water bridges: F:M.189, F:R.194, G:T.199, G:T.199 pi-Cation interactions: F:R.194 Hydrophobic interactions: G:L.116, G:A.159, G:V.192 Salt bridges: G:E.202 HBI.24: 13 residues within 4Å: Chain G: S.187, T.188, M.189, R.194, R.200 Chain H: D.86, E.87, M.88, L.116, A.159, V.192, T.199, E.202 14 PLIP interactions: 6 interactions with chain G, 8 interactions with chain H Hydrogen bonds: G:S.187, G:M.189, G:R.200, G:R.200, H:D.86, H:M.88 Water bridges: G:R.194, G:R.194, H:D.196, H:D.196 Hydrophobic interactions: H:L.116, H:A.159, H:V.192 Salt bridges: H:E.202 HBI.27: 13 residues within 4Å: Chain H: S.187, T.188, M.189, R.194, R.200 Chain I: D.86, E.87, M.88, L.116, A.159, V.192, T.199, E.202 12 PLIP interactions: 7 interactions with chain I, 5 interactions with chain H Hydrophobic interactions: I:L.116, I:A.159, I:V.192 Hydrogen bonds: I:D.86, I:M.88, H:S.187, H:R.200, H:R.200 Water bridges: I:D.196, H:M.189, H:M.189 Salt bridges: I:E.202 HBI.28: 13 residues within 4Å: Chain I: S.187, T.188, M.189, R.194, R.200 Chain J: D.86, E.87, M.88, L.116, A.159, V.192, T.199, E.202 12 PLIP interactions: 6 interactions with chain J, 6 interactions with chain I Hydrophobic interactions: J:L.116, J:A.159, J:V.192 Hydrogen bonds: J:D.86, J:M.88, I:S.187, I:M.189, I:R.200, I:R.200 Salt bridges: J:E.202 Water bridges: I:R.194, I:R.194

10 x K: POTASSIUM ION(Non-covalent)

K.31: 5 residues within 4Å: Chain K: T.11, Q.12, R.14, V.17, G.18 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:T.11, K:Q.12, K:R.14, K:V.17 K.32: 4 residues within 4Å: Chain L: T.11, Q.12, R.14, V.17 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:T.11, L:Q.12, L:R.14, L:V.17 K.33: 5 residues within 4Å: Chain M: T.11, Q.12, R.14, V.17, G.18 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:T.11, M:Q.12, M:R.14, M:V.17 K.34: 4 residues within 4Å: Chain N: T.11, Q.12, R.14, V.17 5 PLIP interactions: 4 interactions with chain N, 1 Ligand-Water interactions Metal complexes: N:T.11, N:Q.12, N:R.14, N:V.17, H2O.33 K.35: 5 residues within 4Å: Chain O: T.11, Q.12, R.14, V.17, G.18 4 PLIP interactions: 4 interactions with chain O Metal complexes: O:T.11, O:Q.12, O:R.14, O:V.17 K.36: 4 residues within 4Å: Chain P: T.11, Q.12, R.14, V.17 4 PLIP interactions: 4 interactions with chain P Metal complexes: P:T.11, P:Q.12, P:R.14, P:V.17 K.37: 4 residues within 4Å: Chain Q: T.11, Q.12, R.14, V.17 4 PLIP interactions: 4 interactions with chain Q Metal complexes: Q:T.11, Q:Q.12, Q:R.14, Q:V.17 K.38: 5 residues within 4Å: Chain R: T.11, Q.12, R.14, V.17, G.18 4 PLIP interactions: 4 interactions with chain R Metal complexes: R:T.11, R:Q.12, R:R.14, R:V.17 K.39: 5 residues within 4Å: Chain S: T.11, Q.12, R.14, V.17, G.18 4 PLIP interactions: 4 interactions with chain S Metal complexes: S:T.11, S:Q.12, S:R.14, S:V.17 K.40: 5 residues within 4Å: Chain T: T.11, Q.12, R.14, V.17, G.18 4 PLIP interactions: 4 interactions with chain T Metal complexes: T:T.11, T:Q.12, T:R.14, T:V.17

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ebenhoch, R. et al., Biophysical and structural investigation of the regulation of human GTP cyclohydrolase I by its regulatory protein GFRP. J.Struct.Biol. (2021)

Release Date

2021-10-20

Peptides

GTP cyclohydrolase 1: ABCDEFGHIJ
GTP cyclohydrolase 1 feedback regulatory protein: KLMNOPQRST

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
a

L
b

M
c

N
d

O
e

P
f

Q
g

R
h

S
i

T
j

GTP cyclohydrolase 1

GTP cyclohydrolase 1 feedback regulatory protein

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