SMTL ID : 2jes.1

Portal protein (gp6) from bacteriophage SPP1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.40 Å

Oligo State

hetero-oligomer

Ligands

13 x HG: MERCURY (II) ION(Non-covalent)

HG.1: 5 residues within 4Å: Chain A: C.55, S.85 Chain C: F.259, Y.260, D.262 No protein-ligand interaction detected (PLIP) HG.3: 5 residues within 4Å: Chain C: C.55, S.85 Chain E: F.259, Y.260, D.262 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain E Metal complexes: C:S.85, E:F.259 HG.5: 4 residues within 4Å: Chain E: C.55, S.85 Chain G: F.259, Y.260 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain G Metal complexes: E:S.85, G:F.259 HG.7: 5 residues within 4Å: Chain G: C.55, S.85 Chain I: F.259, Y.260, D.262 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:S.85 HG.9: 5 residues within 4Å: Chain I: C.55, S.85 Chain K: F.259, Y.260, D.262 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:F.259 HG.11: 5 residues within 4Å: Chain K: C.55, S.85 Chain M: F.259, Y.260, D.262 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:S.85 HG.13: 5 residues within 4Å: Chain M: C.55, S.85 Chain O: F.259, Y.260, D.262 2 PLIP interactions: 1 interactions with chain M, 1 interactions with chain O Metal complexes: M:S.85, O:F.259 HG.15: 4 residues within 4Å: Chain O: C.55, S.85 Chain Q: F.259, D.262 2 PLIP interactions: 2 interactions with chain O Metal complexes: O:C.55, O:S.85 HG.17: 4 residues within 4Å: Chain Q: C.55, S.85 Chain S: F.259, Y.260 2 PLIP interactions: 2 interactions with chain Q Metal complexes: Q:C.55, Q:S.85 HG.19: 5 residues within 4Å: Chain S: C.55, S.85 Chain U: F.259, Y.260, D.262 No protein-ligand interaction detected (PLIP) HG.21: 4 residues within 4Å: Chain U: C.55, S.85 Chain W: F.259, Y.260 No protein-ligand interaction detected (PLIP) HG.23: 5 residues within 4Å: Chain W: C.55, S.85 Chain Y: F.259, Y.260, D.262 2 PLIP interactions: 1 interactions with chain W, 1 interactions with chain Y Metal complexes: W:S.85, Y:F.259 HG.25: 5 residues within 4Å: Chain A: F.259, Y.260, D.262 Chain Y: C.55, S.85 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:F.259

13 x CA: CALCIUM ION(Non-covalent)

CA.2: 3 residues within 4Å: Chain A: E.60, R.83 Chain C: D.262 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Metal complexes: A:E.60, A:E.60, A:R.83, C:D.262 CA.4: 3 residues within 4Å: Chain C: E.60, R.83 Chain E: D.262 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain E Metal complexes: C:E.60, C:E.60, C:R.83, E:D.262, E:D.262 CA.6: 3 residues within 4Å: Chain E: E.60, R.83 Chain G: D.262 5 PLIP interactions: 3 interactions with chain E, 2 interactions with chain G Metal complexes: E:E.60, E:E.60, E:R.83, G:D.262, G:D.262 CA.8: 3 residues within 4Å: Chain G: E.60, R.83 Chain I: D.262 4 PLIP interactions: 1 interactions with chain I, 3 interactions with chain G Metal complexes: I:D.262, G:E.60, G:E.60, G:R.83 CA.10: 3 residues within 4Å: Chain I: E.60, R.83 Chain K: D.262 5 PLIP interactions: 3 interactions with chain I, 2 interactions with chain K Metal complexes: I:E.60, I:E.60, I:R.83, K:D.262, K:D.262 CA.12: 3 residues within 4Å: Chain K: E.60, R.83 Chain M: D.262 4 PLIP interactions: 3 interactions with chain K, 1 interactions with chain M Metal complexes: K:E.60, K:E.60, K:R.83, M:D.262 CA.14: 3 residues within 4Å: Chain M: E.60, R.83 Chain O: D.262 3 PLIP interactions: 2 interactions with chain M, 1 interactions with chain O Metal complexes: M:E.60, M:R.83, O:D.262 CA.16: 3 residues within 4Å: Chain O: E.60, R.83 Chain Q: D.262 5 PLIP interactions: 2 interactions with chain Q, 3 interactions with chain O Metal complexes: Q:D.262, Q:D.262, O:E.60, O:E.60, O:R.83 CA.18: 3 residues within 4Å: Chain Q: E.60, R.83 Chain S: D.262 5 PLIP interactions: 3 interactions with chain Q, 2 interactions with chain S Metal complexes: Q:E.60, Q:E.60, Q:R.83, S:D.262, S:D.262 CA.20: 3 residues within 4Å: Chain S: E.60, R.83 Chain U: D.262 5 PLIP interactions: 2 interactions with chain U, 3 interactions with chain S Metal complexes: U:D.262, U:D.262, S:E.60, S:E.60, S:R.83 CA.22: 3 residues within 4Å: Chain U: E.60, R.83 Chain W: D.262 5 PLIP interactions: 3 interactions with chain U, 2 interactions with chain W Metal complexes: U:E.60, U:E.60, U:R.83, W:D.262, W:D.262 CA.24: 3 residues within 4Å: Chain W: E.60, R.83 Chain Y: D.262 4 PLIP interactions: 1 interactions with chain Y, 3 interactions with chain W Metal complexes: Y:D.262, W:E.60, W:E.60, W:R.83 CA.26: 3 residues within 4Å: Chain A: D.262 Chain Y: E.60, R.83 5 PLIP interactions: 3 interactions with chain Y, 2 interactions with chain A Metal complexes: Y:E.60, Y:E.60, Y:R.83, A:D.262, A:D.262

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lebedev, A.A. et al., Structural Framework for DNA Translocation Via the Viral Portal Protein. Embo J. (2007)

Release Date

2007-03-27

Peptides

PORTAL PROTEIN: ACEGIKMOQSUWY
UNIDENTIFIED FRAGMENT OF PORTAL PROTEIN: BDFHJLNPRTVXZ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

G
G

I
I

K
K

M
M

O
O

Q
Q

S
S

U
U

W
W

Y
Y

B
B

D
D

F
F

H
H

J
J

L
L

N
N

P
P

R
R

T
T

V
V

X
X

Z
Z

PORTAL PROTEIN

UNIDENTIFIED FRAGMENT OF PORTAL PROTEIN

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